iPhone/iPad/iPod Touch apps that use ports other than 80 and friends

Have a look at the ports commonly used by Apple (on all devices, not only iOS) here (Though these are only the ones used by Apple and other Developers might use other ports) and look for specific Services (FaceTime uses many ports, so does Game Center and so on…)

This is a bit off topic but have you considered traffic shaping instead of completely blocking ports.
If you limit the bandwidth lets say after a certain MB downloaded or uploaded via WiFi in a given period of time the students would soon figure out that they are better of using the wired network for their bandwidth intensive tasks.
As you have suggested in your question blocking ports would be an endless wack-a-mole game of user complains and port openings and if a new popular app comes along or Apple changes something in iOS (like Game Center) then you would have to re-analyze your firewall settings every time.

As a sys admin, you would most likely want port 22 open in order to be able to use an iPod Touch SSH app.