Playing MKV from my PC on my Apple TV?

Buy AirVideo for the iPad and install AirVideo Server on your PC. I do this all the time and it plays everything I throw at it, either by directly sending the MP4 file or by transcoding from unplayable formats like MKV or FLV into something the iPad can play. You can then redirect it to the Apple TV. The great thing about this is that I can also set the server to be visible from the internet and then it will recompress material and stream it to me anywhere I can access it so I have full access to my film and TV collection without needing to copy it all over to my iPad. Especially good since my old iPad 1 is primarily used for media these days and it is only 16GB.

mkvs can usually be remuxed instead of encoded to .mp4 much quicker (few minutes compared to a few hours) --
I use XMedia Encode (freeware):
http://www.videohelp.com/tools/XMedia-Recode

I was able to remux 20 seasons of The Simpsons I had (it was in mkv format on my HDD already) in 8 hours not including ripping time (well probably shorter.. i did it over night and did not check it's progress until it was over and by then it had been completed).

Then use iTunes to import and keep it open for home sharing.

For my non mkv / mp4 files I use Air Video as suggested above (the paid version of the app is well worth it)