I used to maintain here a list of all the open source bug trackers I knew anything about, with comments on some of them. Bug trackers are still an active area of development and experimentation, perhaps even more so than version control systems (see ???), and I've found it increasingly unsustainable to maintain an appendix that stays up-to-date with the field. While I have personal preferences — I particularly like Redmine — the important thing is that whatever tracker you choose, it have the features needed to support an active open source community; those features are discussed in detail in the section called “Bug Tracker”.
For lists of bug trackers and comparisons between them, try Wikipedia: Comparison of Issue Tracking Systems.