It all depends what kind of projects you are interested in. And what aspect of it (specific algorithms, UI, networking, etc, etc...)
Head over to freshmeat, sourceforge or ohloh and browse the projects for your area of interest.
Alternatively if you want to look at projects that were chosen for a particular reason google summer of code might be interesting for you - even though these rarely include full projects.
EDIT:
Also alternatively, you might take something like linux kernel, but instead of trying to understand everything try to
- get the big picture
- then concentrate on one tiny piece of it and inspect how the code changed over time (and for what reasons - it should be quite well documented)
