I've used Virtualdub. It's free and pretty good, but I'm not sure about .mov files. It will accept .avi container files with xvid or divx video streams and mp3 (and other) audio streams. You can probably recode .mov files using 'Super'.
Video is a whole 50 gal drum of worms! Have a look at the doom9 site - it's got a lot of guides to video encryption, links to free software and editing:
Doom9.net - The Definitive DVD Backup Resource
Jim