Runaway processes can be a problem in LTSP systems. I've found in particular that Adobe's Acrobat Reader, Firefox, and flash can easily get out of control and suck up 100% of a processor. The cpulimit command (available in Ubuntu and Debian) can limit individual processes by intermittently forcing them to sleep. I wrote a small perl program to watch ongoing process usage and apply cpulimit to out of control processes as needed.
My script, cpu_governor, and the associated init.d startup script are here: cpu_governor.tgz. Let me know if you find any bugs. Thanks.