So it seems like there are many solutions (Boxee, GoogleTV, AppleTV, XMBC, etc) out there for HTPC setups but I can't seem to find a good solution for playing MKV files and I would say the bulk of my video library is encoded in MKVs.
Whats a good solution for an HTPC if I want the following:
Nice to have but not a requirement: - Android Remote App so I can control with my Android device
I would definitely go x86. Right now, I'm using XBMC through my 42" TV and it works great. There's an official XBMC android app, but I prefer using this one. Combine that with a general mouse and keyboard app (I've used GMote for Windows in the past, but have switched to a pay app) and you're golden. XBMC is available on Windows, OS X, and your requested Linux, with packages for a few distros. As far as hardware is concerned, you have numerous options, from build your own to small form-factor PCs.
I would go with XBMC if you just want to be able to play local / network files (not streaming). XMBC supports Linux, OS X, Windows, and the old Apple TV. It has a great system for automatically identifying and tagging your media files, so you can browse your movie with metadata and posters. I've only used it on Windows, where it recently gained GPU-assisted decoding (be sure to enable DXVA in settings). The advantage of using Windows that you can run all of these with a 10-foot user interface:
