Linux

Among these, I prefer Flatpaks the most, with appimages being the second. Though I'd rather use Nix

Flatpaks are insecure by design as they don't cryptographically verify their authenticity after download. Snaps too.

Install with a proper package manager that was designed doe security. Most OS package managers are designed with this.

I've only used flatpak and I honestly see no reason to try anything else. The only issue I've encountered is that Steam games launched by the Steam flatpak occasionally act strange (sometimes they can't locate graphics drivers or connect to online services).

Pacman > Flatpak > won't use it

tbh never looked into snaps flatbacks or appimages. However my instinct as a staunch linux is that anything besides apt-get or apt or aptitude is utter trash. we already have apt, why do people feel the need to divert energies to these unneccessary packagemanagement-fads?

For multiple reasons, I don't use Appimage unless I absolutely have to. I avoid snaps completely. IMO, they haven't been performant, and accessing my home folder requires breaking the sandboxing.

Flatpaks are the only ones I use to any degree, much better experience in terms of adjusting app permissions (including home folder access), and better theme integration.

I don't think I've ever actually found a flatpack in the wild. Not a fan of snaps but have a few appimages that seen to work fine.

Makefile

I prefer the AUR, but if I have to use one of the three it's gotta be an AppImage these days.

I used to swear by flatpak, but because I'm on nvidia it just turns into a stupidly bloated mess since it never removes older driver versions. They're certainly not "bad" though, and I use them on my SteamDeck for sure.

Snaps is too well controlled by Canonical and does have it's limits.

Flatpaks can be very secure, and works in most distros. It is one of my favorites.

AppImages are real easy, and is designed to work on most distros. The only problem is that many apps aren't current. So I don't recommend it unless an app provides it on their own sites. AppImages are often made by somebody else.

Depends on the goal. For systems admin on Ubuntu servers, snaps work well. They have a lot of functionality that flatpak lacks sorely. AppImages are good for seldom used software that is not on the repository. Flatpaks are…functional, I guess. They are boring but inconsistent, at least flatseal helps to mitigate their flaws a little bit. And they are the most end user friendly of the bunch. In general containerized applications on Linux suck ass. All of them. Also, I hate using the flatpak utility, the reverse domain naming is retarded and brings nothing of value.

Edit: I've also noticed that on old hardware flatpaks are horrendously laggy. That might just be my experience but I've not been happy using flatpaks.

i use arch just so i don't have to use any of these

Appimages because I can download them once to my file server and use them several times on different machines. Basically it just works.

Flatpak is fine, it's just at that point why not use apt?

Snap is trying, they fixed the worst problems like performance, storage is still broken.

None. Simply because there is no reason to use em. Thus, user control > everything else -- you won't have that on (any) kind of automated process.

I prefer Flatpaks by a wide margin. This presentation by openSUSE's Richard Brown is a great watch for those looking for a thorough comparison.