I'm on a quest for the same solution. I'm writing my own Twitter client and as it is web based, I develop it from my two computers and run it on my server.

Right now I'm using FileHamster which is quite basic on Windows. I'm probably going to bite the bullet and do SVN or Mercurial. I might do git but I don't want to put my code on github yet.

I'll be eager to hear other people's thoughts as well.