I have students on a small NFS+NIS network. Quotas are enabled and if the user types "quota" on their workstation they can see their status. I created a small script to grab the exit code of quota and to wall a message if they are over.

Since my students are like any other student (unreliable, lazy) they don't bother to check their quotas much and thus what I'd like is for each workstation to run this script every 5 mins or so (to bug them with wall messages).

I could create a crontab for each user, but this is a pita, what with copying over the file, making sure it exists when I create new users etc.

If I put it in the /etc/crontab then it wont run quota for the current KDE user.

What's the best approach to use?

Dunno about "best" but you could retrieve name of current Xorg/X11 display user (PID of KDM/GDM is PPID in Xorg/X11/.*-session DM and the DM is run as the user), get quota stats for that user as root account user, set up Zenity/Gdialog to display warning on $DISPLAY, set up cronjob and don't forget to export DISPLAY variable. 5 minutes seems excessive though. And wy not just enforce quota and let them figure it out by themselves if they hit the limit?..

I agree with unSpawn's last..
quota comes with soft and hard limits. Set those up, add a login msg to mention the limits, then just let them work it out if they hit a limit.