We use JIRA at our company. It's fast enough and very flexible. Here's a question to stimulate the discussion: what would you use if you were a one-person shop or small startup (2-5 developers)?
We too use JIRA and I hate it. Sure it's flexible but that same flexibility also makes it confusing and hard to use. At my last company we used Bugzilla. The UI was ugly but it was easy to grok as a developer and powerful in the way you could construct queries.
We're a 5 developer team and we recently switched from Trac to JIRA. I haven't spent enough time with JIRA to comment on it in depth but it seems pretty nice.
Pivotal Tracker (http://www.pivotaltracker.com)
I highly recommend it, I have nothing bug good things to say about it so far...
Wow. I just looked back an realized I typed 'bug' instead of 'but'! That may look intentional but I promise you it was an accident!
SourceForge Enterprise Edition (now named TeamForge).
Hate it. Would rather be using JIRA like other segments of company are today.
SpiraTeam, and until they fix the speed issues... I can't recommend it.
Lighthouseapp.com works well for me and my team.
bugzor.com (note: This is a site that we created for our projects. Bugzilla worked fine for me before this decision was made.)