LXC for:

• Software builds
• Command line experiments on distros other than my main one
• Running apps with no risk of messes left behind when I uninstall them
• Some (limited) privacy isolation when running apps that I don’t trust

(It doesn’t provide as much isolation as a hypervisor-based virtual machine, but it’s good enough for some purposes, and much better than Flatpak.)

Flatpak for:

• A handful of apps that aren’t available in my distro’s package repo
• Steam, because its runtime containers don’t play well with LXC

(I never run apps from Flathub, because I find they usually come with loose permission settings that sacrifice the user’s security and privacy in favor of the packager’s convenience. Instead, I build my own flatpaks. Some people get a similar effect by micromanaging overrides with flatpak override or Flatseal.)

Snap looked interesting when I looked at it a few years ago, especially since parts of its sandboxing design looked more effective than Flatpak’s. However, it was pushed out to Ubuntu users in a state that I don’t consider fit for release, and the maintainers have been painfully slow to address its issues, and its repository system is not open, so I doubt that it will ever meet my needs.

Docker on some servers, though I intend to switch to Podman. (And you asked about desktop software, so this is a little off-topic.)