Windows server or Linux server?

Depends what you want to restrict, examples? you there are management agents although not sure about management for ubuntu.. what other MS solutions do you have currently?
 
This is for college work. Can group policies restrict users from running programs and changing the desktop on Ubuntu. Or do you use Ubuntu server to do this. Can AppArmor be used to stop users from configuring the desktop on Ubuntu. Currently there are Windows XP and Vista workstations. Maybe Windows server 2008 is used.
 
Windows GPO can't control anything on linux systems, it's specifically designed for windows clients.

However there are third party systems you can use to apply restrictions to linux clients, something like this might be of help.
 
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