Jon Dahl has a great write-up on Rail Spikes comparing Pivotal Tracker to just about every bug tracking application out there.
http://railspikes.com/2009/2/2/pivotal-tracker-bug-trackers
He hasn't had a chance to try it out on longer projects yet, but we use it everyday on projects (like tracker itself) that have been years in development and refinement.
Thanks, Jon, for the thoughtful exploration of the product!