Putting files in folders is a metaphor left over from the way we had to organize physical documents, because we couldn't do any better. The key is to provide easy search and flexible views on top of the data/files users have so they can easily find what they need, not to force users into organizing their files into neat little folders.

OS X gets most of this right because it doesn't care where you put your apps (although /Applications is recommended), applications aren't folder you can mess around with, they are wrapped in a logical package you can move or doubleclick on to open. Spotlight makes it easy to find anything on your computer and most applications are optimized around searching or looking at your data from different views (iTunes, iPhoto, Mail, etc).

I suppose you could restrict programs to only running out of certain folders to centralize it, but I think the only way this kind of thing could ever really get better is a sink or swim approach. As in, if your computer is setup insanely poorly(like if I can't find your programs in the huge mess you plunked them into), don't look to me for help with it, cause I'm just gonna recommend a nuke from orbit approach, with a further instruction to do it right next time. Tough love counts as help, right? Still, I know, I know, it's never gonna happen...