The support System plugin is by far the cleanest and easiest to use that I have found. I do however feel like it is lacking just a little bit.
The one thing it is missing and really needs added is a notes section for each ticket. Notes can only be seen by other administrators. This would be used for site admins to communicate certain things with each other while not allowing the client that submitted the ticket to see it.
If this already there and I just don't see it, somebody please point me in the right direction. If not then I guess Ill get to hacking up the code and see what I can come up with