When I use Fraps in-game, I force the FPS from my normal 60 down to 30; that helps a lot. You could also try recording half-size as well. I would also suggest having a dedicated hard drive just for recording the raw footage, although it probably isn't necessary unless you have a RAID array (I do) and recording to a RAID sux.
But, as has been said, it takes a lot of system resources and CPU cycles to do its thing.