Although I discovered recently that someone had written a Trac backend plugin for Git, which rules. Trac kicks the living shit out of every other issue tracker I have ever seen. You should look into Trac and/or Trac integration regardless of what VCS you us; all useful VC/SCM systems appear to be supported nowadays (alas, no Visual SourceSafe)
Trac kicks so much ass. Moving to Trac legitimately made my hobby site real amounts of money because people entrusted us with more goodwill as a result of our quicker responses and better communication under Trac.
This is just too awesome. Maybe GitHub is truly The Way. I haven't been involved with a Big Project on GitHub yet, only Google Code, so take the following with a metric fuckload of NaCl please.
My experience with Google Code has been closest (in terms of communication and transparency) to that of running my own Trac installation. I assume they're converging towards Trac simply because it's the lowest-effort option at a Python shop with an SVN-centric offering.
Github is neat but I have begun to wonder if Git and its toolchain isn't a little discouraging for new/dabbling developers on a germinal project. I use both, although I'm beginning to drift away to Git for new work. Then again, I've been using Unix toolchains for 14 years now. I'm the target demographic for Git.
Oh, fuck it. This post has just become a catalog of useful links and migration tools for me. If it helps you too, so be it, but writing this much means I have to help myself :-)
trac sucks. Why? It's obviously a pita to configure. Because I've never seen a trac setup work right the first time. Most of the time I either can't create an account to file bugs, or I can't create bugs even though I've filed them. I've never seen trac set up right the first time.
Bugzilla must be better as it generally works.
Lighthouse is confusing ( can't figure out what project I'm filing for. If I file for the wrong one it can't be changed, and where is the search again?)
Mantis is supposedly good. Never needed to use a mantis setup though.