In this article Wilco van Bragt takes the brace lead in explaining why a Terminal Server need to be rebooted. It's always difficult to explain to customers that are new to Server Based Computing. I honestly thought that he was providing a sample reboot script. Turns out he didn't I know I have created my own many times and have seen others. Here are some examples:

Smart Reboot Script 2.0
When the script is launched it will wait for all users to log off the MetaFrame XP server and once there are no users logged on, the server will reboot itself.

Citrix PS 4.5 Restart script
Presentation Server 4.5 reboot script that shuts down all Citrix related services and deleted spool server and temp files. (Dutch) Try this one for Presentation Server 4.0 with advanced logging.

Delete Profiles Script v1.9
This not a specific reboot script but still a very sophisticated script that can help you delete Windows profiles on shutdown.

Dedicated Shutdown Program: ShutdownPlus Pro
There's even dedicated program available to help you properly reboot your Terminal Server farm. ShutdownPlus Pro is the most well known. It is not free.

Login Consultants Solution4 Shutdown script
Ever you ever feel brave then try out Login Consultants Solution4 framework. It has a magnificant collection of scripts including the most advanced reboot script out there. If you can find it...

Happy rebooting!