I am using Git now for working with my diploma thesis and it provides really the best version tracking system. I use the repositories at http://repositoryhosting.com which allows unlimited public and private repositories with Trac for 6$ / month. This is really cheap! And their support is very responsive, the web page light and to the point.
If you have used SVN until now, start using Git. It is worth the effort.
For myself, I now write Comments for my Commits and started to think in patches to a particular problem. I only commit, if the problem I was working at is solved.