The team I'm on currently uses JIRA but I would harshly recommend against using it. It's one of the tools on the belt of the Agile Clergy that is used to beat the peasant into submission. The tool is expensive, constantly deteriorating in visual appeal, workflow, and support, and over complicates very simple tasks. The Agile Clergymen who work at my office boast it's integration abilities, it's high customization, an…
Whatever you want from your tool, the goal is to keep it as simple as possible so you can actually work. If you've got your head stuck in an online system for any length of time during the day, you're not doing it right.
Tools, whether PM tools or not, are supposed to disappear so you can focus on value. If you're talking about them, spending time in them, going to useless meetings with pointless reports generated from them, etc? They stop being tools. At that point they become obstacles. Carpenters don't go to meetings with graphs of how many hammers they own. Brick masons don't spend half a day comparing the status of all of their trowels. Project Management has jack squat to do with configuring and using PM tools. Unless you're specifically training on skills, tools should disappear. That's the entire point. I wish more people knew that.
ADD: Do you know the people who do focus on tools and talk about them a lot? People who don't know what they're doing. To them, the feature list of any tool is reassurance that they can continue not knowing what they're doing and somehow things will still work out fine. The tool will handle it.