Good Video Converters

It seems as though one of the things I've spent a long time searching for is a good video converter I use RipIt (http://thelittleappfactory.com/ripit/) for DVD's because it keeps all the menus etc in tact. I also use MAKE MKV (http://www.makemkv.com/) for Blu Ray's. In particular I'm searching for something that would convert MKV's to MP4's sized for the iPad, Apple TV, etc. I know of Handbrake but I was wondering if there were any other popular choices. Thanks!