Customization available on Jira is Ace.
The main selling point I made to the business was the visibility of the Life Cycle.
Tickets for Features, Requirements and the software tasks combined in one easy to use web based system.
With the SVN integration mentioned above, visibility/traceability is from the feature request down to the code changes (However, this requires discipline or good hook scripts to ensure commits have the Jira ticket id in the comments).
The Fisheye and Crucible plug-ins are another strength of Jira. To see features, requirements, tasks, code checkins and code reviews all in one place is great.
IDE integration is something that Eclipse users can take advantage of, Mylin works brilliantly. .NET VS users, on the other hand, don't have good tools available, yet, problems with ALMs TrackLink tool which is the closest I have found has stopped me integrating Jira into Visual Studio.