The Qubes project is interesting in some ways, but I think they're trying to do too much in one go, and as a result the final product doesn't seem very practical. For example, applications can't use hardware accelerated video according to their FAQ [1].

So pardon me while I braindump...

It would be an interesting project to integrate an Android-style permissions permissions system(possibly using SELinux) complete with per-application virtual filesystems (using FUSE) into the system package manager. So, for example, you install a music player, the package manager sets up a virtual filesystem for it that lets the program see its own configuration directory and your music directory, but nothing else. The package manager asks if you'd like to allow network permissions to the music player (for downloading album art or whatever); if yes, a firewall rule is added specifically allowing that process to access the network, if not, none is.

One problem with that kind of system is that a lot of end-user desktop programs are written with the assumption that the entire home directory is fair game. I'm not convinced that's really necessary, though. In case a program occasionally wants to access a file outside of its normal sandbox (say, you just downloaded a podcast into your downloads directory and want to play it with that music player I mentioned previously) you could always have the supervising program ask the user if it's okay to temporarily add that file to the program's sandbox. If it happens in an expected way (e.g. the user clicks on a media file in the file manager) you could safely grant access to the file without explicitly asking the user.

Something like that, on a distro using Wayland as the windowing system (to avoid the gaping security holes in X), would provide 90% of the security that Qubes does with significantly less inconvenience to the user. It would still require a good deal of work for the package maintainers, but perhaps a distro like that could implement something like the AUR [2] so users could do a lot of the packaging work for peripheral packages.

[1] - http://qubes-os.org/FAQ.html

[2] - https://aur.archlinux.org/