I wouldn't code some of these directly into the help desk system, but rather, make it extendable so you can add some of these as needed:
User/employee "management" -- useful for assigning people to tickets (chain of responsibility/escalation)
An inventory system of sorts -- could be tied w/ a particular customer/user and an IP address even. Good for quick accounting reports on device utilization and IP block usage, and such (per customer)
Ability for customers/users to view reports of their hardware/networks, possibly in realtime and historical (uptime reports, access logs, etc... you get the idea)
Possible links/hooks for project documentation repositories.