I would love to be able to organize my repositories within folders. Right now, when someone views my list of repositories, there is a mix of client side and server side and various technologies. With folders, I could arrange my repos into a client/ folder and server/ folder.

A better example might be a project like ExpressJS. For illustration purposes, assume I wrote it and maintain the repositories for it.

mschwartz/Express/
mschwartz/Express/core - the core ExpressJS
mschwartz/Express/gzip - add gzip layer to ExpressJS
mschwartz/Express/ssl - add https layer to ExpressJS

Or if I want to fork someone else's repositories to create pull requests:

mschwartz/PR/
mschwartz/PR/some-repo
mschwartz/PR/some-other-repo

Backward URL compatibility needs to be considered. Perhaps mschwartz must have every folder leaf repository have a unique name. Thus:

mschwartz/Express/core
and
mschwartz/Foo/core

would be invalid. Only one "core" allowed.

The alternative to folders is organizations, which are way too heavyweight for many uses. An organization for Express as described above is fine, but for PR it seems like an ugly solution.