Obviously, sounds... although not many people actually use saounds at all, I myself always turn all system sounds off anywhere where I have to work on a PC.
And some widgets that show CPU and memory load and whatnot in similar fashion to HUD...
While you're at it, why don't you construct it so that the desktop reminds the Freespace 1/2 main halls so that Barracks enables to change the logged person. Tech Database opens a re-skinned Explorer window with Control Panel, system information and file management systems and all that stuff. Exit would be pretty self-explanatory... Campaign selector would open up a more traditional window where there be all the most used icons like common Windows desktop has.
The main launch door (Continue/Start Campaign) thingy would work as the Start menu button.
F2 would enable some customization window which would let you choose whether you want the system to show Bastion, Galatea, Aquitaine or Psamtik (weren't those all the ships Alpha 1 was ever stationed at in original campaigns?).
...or not. But it's nice to fantasize, eh?
It would be pain to use - or to make it work at all in the first place - in Windows, I know. Possibly customizing some other desktop application in some other system (read: X in Unix/Linux) could lead to more usable results, but it would still result in less than ideal usefulness.
