Here is a command line option that will go through a directory and convert all the mkv's to mp4's with no quality loss and only takes a couple minutes per file. There is a bit of setup to get it to go, but that is a one time thing:
1: install Xcode:
http://itunes.apple.com/ca/app/xcode/id497799835?mt=12
2: install the CLI tools in Xcode: Launch Xcode -> Preferences -> Downloads
3: Install Quartz: (Only required on Mountain Lion I believe, but do it anyway):
http://xquartz.macosforge.org/trac/wiki
4: Install Homebrew:
http://mxcl.github.com/homebrew/
4a: Update Homebrew, open terminal and type the following command (you will need to enter your password)
5. Install ffmpeg (this is what we were aiming for the entire time)
All the above are only required once. What we've done here is setup a repository that will allow you to install pretty much any open source software, then installed the ffmpeg command that is going to do all our magic.
Now just run this command (remember to change the directory name to the one that has your mkv's in it)
Code:
for f in <DIRECTORY>/*.mkv; do ffmpeg -i "$f" -vcodec copy "${f%.mkv}.mp4"; done
you will have to run that in each directory with video files, it doesn't go through sub-directorys. However it will convert all your files with no loss of quality. A little work, but still easier than going file by file with some of the other methods