I think the "Support Request" feature within JIRA's administration interface is great. I only wish the email it sends to jira-support could be sent from a different user than the default outgoing email user.

We use JIRA as a helpdesk ticket manager as well as a development issue tracker. Accordingly, we've set the outgoing email address to match our incoming helpdesk mail handler queue. That means that whenever someone at Atlassian replies to one of our support requests, an issue gets created in our helpdesk project regarding that issue. This isn't terrible, since we usually just move the issue to our JIRA project (where we handle issues related to jira itself) and then link them to the issue we created on our end that corresonds with the support request.

Hmm... another way to deal with this would be the ability to associate a support request with an existing issue so that replies would be attached to the right issue.