Until recently I had been able to use Quicktime 7 to perform a passthrough encode of MKV to MP4. Meaning there is no need to re-encode audio/video. This means you can convert an hour long MKV file via pass through encode to MP4 in about 30 seconds instead of having to use something like Handbrake to do the same thing and having it take 30-35 minutes. Quicktime 7 handles it if you have Perian installed. It seems like mtn lion is not supporting the last build of Perian so I am looking to see if anyone has a different method for doing this.