I used to use a spreadsheet and/or separate text file per project (I had the same problem with todo comments you list; they're local to the code, and if there's an issue that's not local, it tended to slip through the cracks).

Recently I've set up a [Redmine][1] server on my home network. It's a bit heavyweight for a "team" of one, but I'm working on quite a few projects on my own time, and tend to just use the Issue Tracker + Repository options with maybe the odd wiki page in more complex places.

A friend of mine swears by [Pivotal Tracker][2] for the same purposes, but my current employer uses Redmine internally, so I figured this would give me some practice. It's not bad.


 [1]: http://www.redmine.org/projects/redmine
 [2]: http://www.pivotaltracker.com/landing_page