1) WMI methods. Install/uninstall MSI, start/stop services, create/kill processes, etc. I know this can be handled through scripting, but having it built-in would save alot of time.
2) Ability to select multiple computers to run an action against.
3) SNMP functionality. Being able to see what network printers are low on toner or have other errors is a must. Viewing the status of various routers would be handy, as well.
4) Custom run-once reports built into the webpage.
5) Role-based access. Some people we want to be able to look at the information, but not run actions.
6) Software deployment. This would really just be a combination of 1 and 2, but on a larger scope.
I'm leaving helpdesk off my list because we already pay for a decent one, and our office has been using it for too long to switch to something else.