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).
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).