[janvanmaar]

You can use your OS to alter the priority of the processing that are running... (renice from command line or some GUI utility). Of course I am aware it would be much more convenient if Calibre spawned the processes with the priority you want directly - perhaps with some help of the Calibre developers it would not be that difficult to modify the code so that Calibre spawns processes with lower priority if that is important for you... or perhaps just as a quick hack you could write a tiny script that checks the processes say every 10 seconds and renices the Calibre ones...

EDIT: in any case, I would first try running a few long, CPU intensive conversions using renice (or something similar) and see whether it actually solves your problem - if so, then you should be able to apply some solution (either one of the above mentioned or something else)