I haven't had much experience with any of the ticket applications, other than from a client standpoint, but today I saw what Avid Software is cooking (IntelloDesk support software) and I was extremely impressed with it!
Use Modernbill personally. But thats a bit on the extreme as far as just getting a support desk going. Cerberus and Kayako are the most common. Go with them just because of the support.
I've used perldesk, modernbill, clientexec, but I just found about Cerberus it looks VERY impressive I'm definetly going to be giving it a try thanks for the information Dactyl.