Until recently, I hated Jira, but my current company uses Jira + Greenhopper, and I actually really like it. Greenhopper gives you a sort of PivotalTracker like interface, except that I've always found PivotalTracker to be a good idea, poorly implemented.

We also use Crucible, which is a great code review tool, and Confluence, which I don't really care for, but I don't really dislike it any more than any other wiki software.