I like it

.
You may want to change the command to
@="\"C:\\Program Files\\Serviio\\lib\\ffmpeg.exe\" -i \"%1\" -c copy -map 0 \"%1.mp4\""
This will copy all video and audio streams (as opposed to only the first one of each) and any other embedded streams (subtitles etc). I have pretty much converted all my MKVs to MP4 for better "playability" on the PS3 (my other devices either support MKV and MP4 equally as well, or as poorly as one another, so it doesn't matter to them).
Also, should have mentioned (free plug

) - as a Windows user you can use my tool here:
viewtopic.php?f=17&t=12136 which supports bulk remuxing of files. On the remux tab, drag and drop your files, select "Remux from MKV to MP4" and press Go!. This tool does a lot of other things (sleep management, automatic library refreshes, etc) - if you dont want to use the just ensure you untick "Start on logon" on the settings tab.