You need MKVtools my friend. Converts in about 5 minutes. Actually it just extracts the video and converts the audio and puts it in a nice m4v package.
I agree with dawgfang, MKVtools is awesome. I also use Subler, as it handles the metadata end of things. You could just use Subler alone if you need a straight mkv->m4v but I usually want to add and/or convert audio.