Convert a bunch of MKV files to MP4 to read them in iTunes
Install ffmpeg by running brew install ffmpeg or sudo port install ffmpeg or by downloading a binary from http://ffmpegmac.net. Then run a command like:

for f in *.mkv;do ffmpeg -i "$f" -c:v copy -c:a aac -b:a 256k -strict -2 "${f%mkv}mp4";done


Or if you don't need to re-encode audio:

for f in *.mkv;do ffmpeg -i "$f" -c copy "${f%mkv}mp4";done