What platform? I assume from "crontab" that you're on Linux, in which case you can run ffmpeg using nice. That is, instead of:
ffmpeg (options)
Run:
nice -n 20 ffmpeg (options)
This will run ffmpeg at the lowest possible priority, which means any other processing (e.g. web pages) will get scheduled ahead of ffmpeg. It'll still run at "100%" but it'll never take time away from higher priority tasks, which is what you want.
Dean Harding
2010-05-31 23:44:10