I’m a fan of Pivotal Tracker for small teams using Scrum. I haven’t used it in a few years, but I don’t think it works well for large teams...I need to revisit.
IMHO, Jira is awful. Looking forward to the other responses.
Same. Pivotal is nice because there's very little to bikeshed, but it's a double edged sword because it can't evolve as your processes get more sophisticated.