You may be interested in AppDirs, and ROX in general:
http://rox.sourceforge.net/phpwiki/static.html
However, if you see only one file for an application, it is almost never the reality. It is rather a display "trick", to improve usability, and simplify things. Other files are actually there but you don't see them.
Another project that may interest you is GoboLinux:
http://www.gobolinux.org/
It is probably more complete, as it is an entire Linux distribution.
Yves.