A-tier
Exotic Crystals. I like this. Exotic items are generally better and yield more energy, but there's some huge downsides like losing important items (transmutation, invis, etc) and cluttering the bag. It's probably not worth spending the energy cost to +3.
Mossy Clump. Water and especially grass floors are useful. Not worth upgrading to +3, as by the time you can pay the astronomical 81 energy, you have explored more than half of the dungeon. You can refund the cost if you energize the seeds you get from trampling grass, but you'll need to burn over 40 seeds. It's only worth upgrading if the game is longer.
Petrified Seed. Another favorite, as seeds are unusable with challenges. Somewhat worth upgrading to +3, but only if you can pay the energy cost early. In general, trinkets like these should only be upgraded if there's many more floors ahead.
Mimic Tooth. Dangerous, but gives more rewards in return. Very interesting and I love it, but the mimics are deadly later in the game, and at that point you can throw it away.
B-tier
Wanderous Resin. Can be fun with mage, but some effects will destroy items and damage the user. This trinket icon should be changed, as all the catalysts, resins, dust and moss in the game is hard to differentiate for colorblind users, they all look like the same hairball.
Salt Cube. This one's weird. I think it's below C-tier on normal gameplay, but shoots up to high-tier when playing with many challenges. Fast health regen is much more important and satiety is never an issue, so I always avoid taking this when I play normally, but it's useful when doing the diet challenge. The buff to 40% finally made it okay-ish in normal gameplay.
Eye of Newt. Kinda useful with darkness challenge, you can constantly throw and pick it up to adjust the vision, but can be annoying.
Shard of Oblivion. The drop boost is not that great, but it can make getting loot a little easier. The unidentified gimmick is an interesting downside, I like how the shard can identify items that are ready for it.
C-tier
Parchment Scrap. Purely advantageous at +3, but it's too costly and equipment drops are too rare for this to be useful. I think getting enchants normally (with arcane stylus) is cheaper and better. It could've been good if you can combine this with mimic tooth.
Trap Mechanism. You can kill enemies with traps and pitfalls, it's fun but I'll only take it if I have blast wave early, and that is very rare. This trinket got more dangerous without disarming.
Dimensional Sundial. Only useful to speed up ring of wealth farming runs, and the energy you use to decrease enemy spawn rate should just be used to create helpful items, to combat said enemies. Could use an additional effect.
Vial of Blood. Very harmful downside and the extra healing is not necessary on normal gameplay. Might need to be less severe, the immediate potion heal is too important to prevent deaths.
Rat Skull. Only useful if you want to collect rare bestiary monsters. You need to find crazy bandit, chaos elemental, and crystal mimic for it to be useful, because their drops are the best, but it needs too much luck.
D-tier
Chaotic Censer. You use up items for puzzle rooms to get a magical catalyst in a treasure box, spend energy on it, only to get a harmful challenge that can kill you and destroy items? The gimmick looks fun, but not knowing when it will activate is too dangerous.
13-leaf Clover. Needs a more interesting gimmick. It doesn't matter if you roll high or low, it will average to the same damage as the game progresses, so ultimately it doesn't have any usage. The trinket has a very specific use if you equip +0 fast weapons against highly armored enemies, it can overall deal a little more damage, but the usability of this trinket sharply decreases when you upgrade your weapons. It's also too dangerous if enemies can do high rolls to you, it's probably best for it to never happen again.
I've noticed it too. Most trinkets are definitely a beginner trap as you've said, they need to spend energy on alchemy recipes instead of using all their energy on "just for fun" trinkets. For advanced players, energy economy becomes very important with challenges, I squeeze every energy I get from profitless items like stone of intuition's second use, detect magic, certain seeds. There's no room for +3 trinket energy, I often keep them at +0 and energize it later, or immediately throw it away if it's harmful.