I use Axosoft Ontime, it is specific to software development, has feature and defect tracking, help tickets, email integration, and is very customizable. Check it out
Bug Tracking Software by Axosoft Defect and Issue Tracker HelpDesk
They have a free 1 lic deal, fully functional, which I used on my desktop for years. However, obviously you cant colloborate with team members. I am a freelance developer, so initially sprung for the hosted version for the customer portal interface for my clients. It is pricy, but it is great, nice AJAX interface for an almost pure desktop flexibility.
john