Bundled Applications for GNU/Linux?

munehiro asks: "As an addicted GNU/Linux and Mac OS X user I recently tried to install binaries and libraries on a Linux box using an approximation of the elegant and clean approach known as the Mac OS X bundle (everything about each app or lib under a different directory) as opposed to the Linux standard approach 'everything under a common prefix' (normally /usr or /usr/local) with applications and libraries mixed in the standard subdirs bin, lib, share and so on, and found administration life much easier. What do other, more experienced readers think about the problems and improvements related to dropping the current Linux approach for a 'bundle-like' one in Linux distributions?"