Sort of like SilentPanda except I break out my Documents folder by document category - Current Project, Presentations, Personnel, Customer Support - that type of thing.
Under each of those are more individual folders of folders of folders of documents. It makes sense to me 😉
Edit: Just realized you asked about keeping extra crap out. Well, the big things (movies, music, pictures) tend to be in folders that I can easily peruse to see if there are "extras." Other documents don't tend to take up a lot of space, so I don't worry about them. Every once in a while I'll do a find for large files and see if there are any I don't need, but I've never filled up more than about 75% of my HD, so I don't worry about it too much.