After searching high & low for a bug tracker to use, I have finally settled into Trac, but only recently I have had the time to really take a deep look at it. The #1 issue with Trac is that it is hard to setup for the first time. I am used to web applications that are either drop in (ScrewTurn Wiki) or Drop In, mess with config, done (just about anything else). Trac has a very different approach, in which most of the management of the project is done via a command line tool. It took me a while to grasp that, and then it was a lot easier. (Yes, I know about web admin).
The #2 issue with Trac is the version number, it is currently 0.10.2, for a product that is feature rich and stable enough to call 1.0. I am used to OSS projects have ridiciously low version numbers, so it is not surprising, but I do believe that this would be a turnoff for many people. I believe that the low version number is because they are making breaking changes to the code base fairly often.
So far I have been very impressed with the amount of stuff I can do it. It is highly customizable via configuration, and there are all sort of really interesting plugins that exists for it. Gantt chart and export as PDF are the ones that are really cool. But there are others that seem to fit just about any concatenation of features that I can think of.