Flatpak is my preference since it supports multiple remotes (repos) and sandboxing. With flatseal tweaking the sandbox is also easy.

Snaps work great on Ubuntu and support cli tools as well as system components. But their sandboxing doesn't work on many distros and the one and only repo is controlled by one company. If I'm not on Ubuntu, I don't see any reason to choose it over flatpak.

Appimages are great for putting on a USB stick or keeping a specific version of software. But I want to install software from a trusted repository, which Appimages support at best as an afterthought.