There is a tool that will remux (not re-encode so no loss of quality) from .mkv to .m4v Apple compatible format. It will even add an AAC 2.0 track so you could play it back on an Apple mobile device while keeping the original audio. It will also add cover art and tags for iTunes if you like. You can get it here http://www.videohelp.com/tools/MkvToMp4. I highly recommend it.
I've been using a PS3 for a while, transferring the converted MKV files (now M4V) to my PS3's hard drive. I've been thinking about getting rid of it and getting an Apple TV since I don't play games much anymore. If I convert the MKV files to M4V like usual, will they stream well enough over Wi-Fi to the Apple TV? I've been considering a Roku as well, just for the USB drive. But if the performance is good enough with the Apple TV (streaming a movie from a wireless Macbook Pro to an Apple TV that's connected via ethernet) then I'll go with that, since the AirPlay functionality could be neat too.