There's a few listed here:
Top > Customer Service Solutions > Help Desk & Ticketing System - Hosting Software - Webhosting Solutions
You can probably integrate / bridge most of the more popular ones with other CMS solutions with a bit of hacking, though there maybe plugins / extensions to do it.
I think there's even an extension for vbulletin that can handle helpdesk stuff, though I've never had any need for it personally