Disclaimer: i also love playing bobylev versions and a bit of scorched, this just happens to be the version i've got a lot more experience with.
Spoilers for the entire game.
Sewer normal enemies:
The marsupial rat is your most basic "fodder" enemy, perfect for introducing any new players to the combat system and somehow remaining fresh and complex threats for veterans by being the baseline of how enemies can change via challenges (most notably with HC on, but even more subtly like FiMA making everything hurt more or OD making your natural regeneration a much more drainable resource)
alongside the rat, you have the sewer snake - a great way to introduce the player to the invaluable nature of sneak attacks (or higher-accuracy/guaranteed hit attacks like the bow at a distance or a wand zap), while being weak enough to only require 1-2 hits if handled correctly. the only flaw i can really see in it's design is how a giant-championed snake could pose an unnecessarily hard challenge for particularly the warrior, as he has no real reliable baseline method of taking it by surprise or high-accuracy attacks at the start without doorways or corners to run through - both being massively complicated by the snake not having the ability to pass through narrow areas.
Gnolls act like a direct upgrade in power to rats, but give gold sometimes - an important signal to newer players that sometimes the enemies they face will end up rewarding them for defeating them in ways other than simple room progression, all while keeping the general difficulty aligned with what the average player's equipment would be for the area.
Flies act as a secondary tutorial to sneak attacks if the player is willing to experiment enough in combat with them (hitting the split-off flies the moment they separate from their main cluster) as well as a subtle encouragement to start using narrow paths as a risky (you can get sandwiched between 2 enemies) but rewarding (you can only have to deal with 1 enemy at a time as opposed to a cluster of them at once) melee combat option, while also being a reliable source of invaluable health potions for newer players. My only major issue with any later-game impacts they can have is when they're blazing. Blazing flies can ruin even the most well-prepared run if there isn't a source of water or escape route available, while being very difficult to brute force your way through given the sheer overwhelming damage output a single swarm can have - even on death. There are ways around this and blazing champions in general can always be useful to the player as well, with the on-death aoe igniting their neighbors if positioned well enough - but that just isn't enough to compensate for the damage these can do to an otherwise good run.
edit: (the blazing issue is massively toned down, the only other problematic fly type i can think of is giant and even those can be avoided for the most part by not splitting them.)
Sewer crabs can challenge the player with not running away or baiting doors too much thanks to their increased speed, while still crippling themselves because of it - they're easy to lure away from their own allies even if those allies are also awake and know of your presence. Overall they serve well as extra difficulty ramping and another teacher for singling out enemies. Despite the obvious "blazing crab scary" jokes that a lot of people - even myself - have made, i personally believe that projecting crabs are an even bigger threat. This is because crabs already have a slightly more-than-solid damage output and giving them a buff to that while also making them stay the furthest back in their pack can significantly increase how much damage they can deal to even an experienced player.
edit: (This has largely been toned down with the nerf to projecting enemies, no longer a problem. The biggest crab issue i can think of now would likely be blessed ones due to their massively increased consistency, given how solid their stats are already.)
Slimes are a very good teacher of how sometimes raw damage output just can't help you alone - they have respectable damage output and can't be killed in just 1 blow or 1 turn, you need to get creative with fighting them. For instance, a new player could have learned by this point that traps can be used in their favor if an enemy is closest to it, so they could set off a poison dart trap and watch the health of the slime they feared so much whittle away in just a few turns.
Sewer Variants:
Albino rats serve as a light introduction/foreshadowing to the fetid rat and the idea of other rare enemy variants while posing some reward for getting defeated - food.
Caustic slimes do the same for Goo, and could also serve as a subtle hint that alchemy is more of a major mechanic than one would think at first with their goo drop, since the albino rat gives such a staple item as it's drop and the caustic slime gives an alchemy item, then surely the alchemy system must be a staple in some way too right?
Sewer Minibosses:
The fetid rat serves as a mild introduction to the Ooze status and the idea of keeping away from your enemies if they're overpowering in melee (the stench acts as a sort of parallel to Goo's pump-up) while being entirely forewarned by the sad ghost (it telling you to avoid the stench)
The gnoll trickster serves as a temporary introduction to enemies that can attack from more of a distance, while having a very simple counter (not letting it run away from you). This especially helps because the next enemy with any ranged capabilities outside of Goo would be DM-100, who follow the exact same idea save for trying to fight with weak melee attacks if brought within range instead of running. The trickster can also be cornered with some dungeon generation luck, leading to the primary challenge becoming herding it into a place it can easily be killed - rewarding smart movement and planning from the player.
The elder crab serves primarily as a sort of "ultimate" sneak attack tutorial, while also being easy enough to conquer if you manage to get your hands on a beehive or stone of aggression that early, rewarding deeper knowledge of the game and expanding your ability to work around it as opposed to having the same 1 solution always.
Sewer boss:
Goo takes everything you learn in the sewers (avoiding the "stench" of power buildup from it's charge-up attack, landing sneak attacks, cleansing yourself of the oozed status) and challenges you as a major test for all of them combined. Assuming the player doesn't already know about how breaking line of sight immediately cancels the charge-up attack, they could try to outrun it and only barely escape the blast. The oozed status it applies on hit can easily be cleansed if you occasionally step in water, but it will do the same, and it will heal from doing so as a sort of punishment to those who linger too long in water (and they can try to stay in a tile of water while goo is on dry land, but thr pump-up will put a stop to that, forcing them to relocate and forge a more reliable strategy.)
Even if you're a veteran fighting goo, you still need to be vigilant and dodge it's charge-up via grassdancing or turning a corner, since it still deals massive damage and cancels it's related challenge (slime janitor) if you allow it to use a pump-up at all, as well as it's aquatic healing doing the same which puts you on a defacto timer if you want to get it (the timer being your health, ticking down steadily with the oozed status) that can only be rewound by consuming precious resources or slowed down by stepping in water, which becomes massively risky as it's next pump-up attack will become the last - for either you or it. (assuming you aren't using the rogue's cloak for a sneak attack chain)
Goo also encourages the use of throwable weapons the most out of any sewers foe, as it has no option for ranged attackers outside of blindly approaching them - this works in tandem with it's non badder bosses charge-up attack having enough time to allow the player to gain a bit of distance from it on escape, letting them throw something at it for the reward of having shaved a little off of it's health bar.
Prison normal enemies:
Thieves can make the player start trying to delay melee combat for as long as possible until an enemy reaches them, an overall useful practice that further encourages the use of throwing weapons for specific enemy encounters. Personally, though, i have an issue with how they can take Ankhs in particular - a new player might get unlucky and have their ankh stolen right before death, then think "Wow, that thing didn't help me at all! i better not waste my money on such an expensive dud next time!"
Even still, thieves can serve an alternative purpose opposite from crabs in the sewers - posing a difficult question to the player. Do you want to get your stolen item back and risk following the thief into a probable enemy-filled room? Or do you want to leave the thief for now, letting it get away with your item in exchange for your ability to handle the upcoming room as best you can under less stressful circumstances?
In terms of veteran play and challenges, the most issue most people have with thieves is when they're given the projecting champion title. Projecting thieves can show up at the opposite doorway of a room you're in, take an item of yours, run away, and repeat until they're caught.
edit: (this has been fixed with the projecting champion nerf! Another threatening thief type is likely blessed since they can avoid you for longer and will very easily steal items on their first few hits.
Skeletons serve as the sort-of upgrade to gnolls in the sewers, never truly not being a threat since they have such solid stats. They also serve a new challenge and tutorial to some specific enemies having a last-resort style attack, in the form of their bodies exploding in a small aoe near their re-death site. This encourages newer players to stay as far as they can from a dying skeleton if they want to take minimal damage, but also poses a rather niche use similar to blazing champions in general - hurting the enemy's allies by their own reckless attack.
Skeletons in general pose a massive challenge in most runs surrounding FiMA since their death explosion is very hard to avoid reliably and can deal massive damage if their target has little to no defense (as is the case for anyone at all with the challenge enabled) so some rework may be in order, like one i've mentioned before where they could amplify the next hit you take in a short time by some decent number instead of dealing extra direct damage on explosion, to punish the player recklessly running into the next room/enemy immediately after a skeleton while still preserving it's useful qualities in both teaching newer players and being indirectly helpful to experienced ones.
DM-100s force the player to think a lot more about how they approach groups of enemies, as they will need to draw in the machine before anything else or suffer the constant heavy, armor-piercing, accurate damage they can throw out from a distance. This gets complimented by their rather weak melee attacks, showing that closing the gap 1 way or another is truly the best say to handle an encounter with them.
With challenges enabled there's a single issue i can see with DM-100, and that's blazing. Blazing enemies explode into 3x3 fire when they die, and DM-100s' normal drop is random scrolls, which will immediately burn up if they're blazing. This makes fighting a blazing DM-100 less rewarding than a normal one for most purposes besides just getting it out of your way.
edit: (blazing champions' nerf has fixed this by providing a way to avoid the scroll getting burned up / the fire spawning entrely, that being killing the DM-100 on water tiles.)
For experienced players, they can pose a very interesting - albeit still workable challenge if there is a prison guard in the same room, but decently far away from the DM itself (see below for details)
Prison Guards actively work to close the gap between them and the player, forcing them to have enough upfront melee encounter skill and power to fight through them or enough ranged attack potency to finish them before getting drawn in. The chains they wield being able to cripple the player also helps discourage over-use of the sneak attack mechanic, since you can't just endlessly run through doors if it catches up to you repeatedly.
This compounds well with the above scenario involving DM-100, since then the player (if drawn in by the guard) needs to either: -Get behind the guard in a way that forces the DM to approach and get in melee range, then fight both in melee simultaneously -Finish the DM-100 with a particularly strong ranged attack before it can deal too much damage, then fight the guard in melee -Approach the DM-100 initially, costing extra turns due to the guard having crippled them but allowing them both to be taken head-on again -Use extra resources they found to escape the situation and recover elsewhere, or reposition for a better angle of attack than they previously had
Overall, guards can do a lot to force the player into very uncomfortable, unusual or otherwise undesirable situations that they need to get creative to escape from intact - even for veterans.
edit: not a correction, but i feel like giant guards can be particularly powerful as their already very solid and tanky stats get boosted by extra reach, effectively turning the guard into a proto-golem.
Necromancers summon endless skeletons to deal with if you don't challenge them head-on or find a position that locks their summoned skeleton from being able to reach you, providing a sort of ignore-the-fighter, hit-the-healer fight that no other enemy in the game can provide, while also rewarding the player with more precious potions of healing if they succesfully take on this new and different threat.
In higher chalenges, necromancers can become particularly brutal because of how taxing skeletons can be to certain challenges already on their own - FiMA for instance. Champion necromancers also pass on their title to any skeleton they summon, proving that skeleton to be a high priority target if you can't access the necromancer in a given moment.
Prison variants:
Bandits pose a much greater risk/reward than thieves, however can do some massive damage if not handled properly - especially if other enemies are around as they land a succesful hit on you. This works well enough, however, due to their frailty thanks to being a thief variant.
Shadow necromancers emphasize the classic necromancer's hit-the-healer concept to an extreme: hit the healer before it out-summons you and surrounds you in wraiths. In exchange for this even more unique challenge, the player gets a 1-use save from having equipped any cursed item, a great reward for a very challenging enemy.
The only major issue i see in Shadow Necromancers is that they can be Blazing champions, for 2 reasons: 1 - the wraiths will all explode into fire as well on death, not to mention set you alight with every hit. 2 - the necromancer's scroll is all but guaranteed to be lost because of it's immediate fire spreading on death, similarly to blazing DM-100.
edit: (both of these issues have been alleviated by the blazing champion nerf!)
Prison Minibosses
The corpse dust's graveyard is noticeably different from all other locations in the prisons, and provide you with a sense of danger due to sheer unfamiliarity alone - which is immediately proven to be warranted with the skeleton(s) resting inside, as well as the wraiths that constantly come from the corpse dust as you hold it. The dust itself provides a sort of escape-rush feeling to the player as they get quickly surrounded by wraiths, and need to give the dust to the wandmaker as fast as possible before they get consumed by the amount of vengeful spirits that truly want that dust to remain their own.
For veterans, the corpse dust is well known to be an easy gateway to a necromancer build, provided they already have a stable source of wand charges and a non-wandmaker wand of corruption.
The rotberry plant (i am assuming post rework for this, see evan's update sneakpeek if you haven't already) room makes you deal with enemies that are stationary and avoidable, but still a major hazard and very deadly if mishandled. The heart itself forces you to kite it's gas in a very confined space assuming you didn't kill any vine lashers, leading to an interesting minimal-scale battle scenario. This all happens while you must contend with any enemies that happen to walk in on your little seed-harvesting mission, which further complicates the entire ordeal.
For veterans, the seed can pose alternative uses like for the warden (+1 strengty temporarily as well as renewable toxic gas cloud generation), footwear of nature (renewable ranged toxic gas cloud placement) or in alchemy with a blandfruit (permanent +1 strength to equip upgraded gear a whole tier earlier than usual) as well.
The newborn elemental is a mini puzzle (in a non-obnoxious way, as if you don't already know the answer it's relatively simple, while if you do it's very quick to solve) to fight, while providing a tough challenge to those who didn't have the resources to freeze it. (this also, by the way, serves as a tutorial for elementals down the line too)
The embers it drops can also be used to summon an elemental of your own, which can definitely help carry you through the fight with Tengu and the caves all the way to the early dwarven city.
Prison boss:
Tengu's design rewards 2 things primarily; haste and forethought. You need to keep the phase 1 traps in mind as you navigate your way towards him, but must do so quickly as every turn spent is another suriken to your torso.
In phase 2, after being whittled down significantly, tengu gives you a moment to rest before opening the door to his next phase in which he throws multiple new attacks your way that force you to think and adapt very quickly to what he does next, or else you take large amounts of damage or get a very harmful debuff (fire)
This gets emphasized by the Prison Warden badge's challenge, in which you need to know all about what tengu does and how to best deal with all of his tricks - even if your initial attempts to dodge them won't work. This subtly teaches the player to bring backups for every major encounter they face incase their primary plan doesn't work, what Goo did with forced repositioning but taken to a whole new level.
As a veteran player you become able to sometimes take advantage of his phase 1 traps by using a Talisman of Foresight on them - leveling the talisman up significantly, for just a few turns of shurikens in exchange.
Misc. enemy/variants:
Piranhas teach the player 2 things: Sometimes, conflict avoidance is the best option (sneaking past them in flooded treasure rooms) and sometimes you can take down powerful enemies with an achiles-heel or 2. (pulling/confusing them onto land, attacking them from where they cannot reach) In exchange for exploiting a weak point in an otherwise very powerful enemy, you get food (always a good thing)
Phantom piranhas help ensure both of these are taught much better, as you can't exactly cheese a phantom piranha, but they give an even greater reward upon being killed (phantom meat), showing that you can still get a proper and worthwhile reward if you're ready to hunt one, but if you aren't, you need to once again simply avoid conflict for the best result.
Wraiths serve as a great baseline risk to the reward of looting corpses or tombstones while also keeping the idea of sneak attacking and the optimization of such as fresh as possible in the mind of the player.
Red wraiths further this goal while also providing a workaround for those who want an extra reward as a sort of tradeoff - uncurse the wraith and save it while consuming a scroll of remove curse, get a piece of equipment that is guaranteed not to be cursed.
(personally, i think red wraiths should be guaranteed to drop at least +1 equipment on cure as well, but even as they are now it's a good way to get equipment if you're particularly starved for it early on.)
If you disagree/agree with any of my takes here, feel free to comment about it! I'm open to discussing anything here and just wanted to make a sort of open-love-letter sort of thing for SPD. Discussion about it would almost surely help everyone involved learn something.