The trick is not to watch the movies transcode in Handbreak. Start a cue of a few movies, then go to sleep or go to work.I just tried Handbrake converting down to MP4 and it took forever on a Wintel 7 notebook.
It will take you 5 minutes or less of your time to set up the cue and the rest of the time it takes to transcode will be be computer time, not your time. Make it a daily ritual and you'll be done before you know it.