From Joel Spolsky and the team at Fog Creek Software comes FogBugz, probably the best bug tracking software package available.
FogBugz manages projects, tracks bugs, and even tells you when you’re going to ship. It includes an issue tracker, advanced project management and scheduling, a wiki, and customer support features like email routing and discussion groups. It is completely extensible with plug-ins and an XML API, and integrates with all major version control systems.
Other than just tracking bugs (which it does a great job of), it also supports wikis and discussion groups and tracks customer emails. I have to say though, that the coolest feature of FogBugz would have to be their use of evidence based scheduling: FogBugz tracks how you fix bugs and implement features and will report if you are on schedule to meet your release date, and what your probable release date is.
The Student and Startup edition has only one limitation that you can only have two users. In most cases, if you’re reading this, that’s probably not an issue at all. Other than that, it is a fully working version of FogBugz OnDemand (their online, Fog Creek hosted service).
The Student and Startup edition of FogBugz can be found here. It can take a little bit of digging around on the site to find, but it’s there.
View the complete list of awesome tools for developers: Free Professional Tools for Startups