OK, most people who aren't unix elitists have realized by now that application-per-directory is much better than a whole slew of seperate hierarchies like /etc, /usr/bin, /usr/share, etc. I've recently looked at The ROX Desktop Environment, which claims to have such app directories, but it doesn't take it near as far as it _ought_ to go. The cool part, though, is that the Rox package for debian installs a menu-method which automatically generates these App directories when you install new debian packages. Unfortunately, the app-dirs it generates are quite minimal. All they have is a script that executes the program, a symlink to the /usr/share/doc/, and an icon file.
I'm considering hacking on Rox's menu-method to be a bit more robust. Not only to contain an executable and a link to documentation, but also to the shared-data directory (/usr/share/) and the system configuration file for the application. Also, with manual maintenance per-package, there could be symlinks to user configuration files. This'd be a much more complete emulation of Application directories on debian.
I'm also thinking about writing some scripts to deal with these application directories nicely, for example, an 'edit-config' script that automatically used CVS to do versioning of your config-files. that would kick ass. =)