Do the Evolution has always been a personal favorite of mine, that might be the most underrated PJ song.
Hard not to go with Black... Black is kind of a religious experience when you see it live, imo.
Betterman, Daughter, Corduroy, Nothingman all up there for me... It also occurred to me reading through this thread, and clicking on Hawg's links -- PJ might be one of the most fun sing-along bands of all time - something about Eddie Vedder's voice is fun to try and imitate.