Mine is extremely messy at the moment; it's currently centered around what sort of VCS I decide to use / pull code from.

With that said:

~/repos : root directory of all of the repos I'm using.

~/repos/git

~/repos/svn

~/repos/cvs

...

And then underneath those, I have a smattering of repos from various sources. It's ugly as hell, and I'm really liking this thread mostly so I can get a better idea on how I should reorganize my stuff. :)