I think it would be ideal if I put a new MKV file in a folder, my file server will check every XX amount of time, use XenonMKV in command line mode (output into another folder that's shared to my 360), delete the source MKV file. Life is great...

I second his request. I've been trying to find a way to automate this whole conversion process, and can't find a single program that will do it. Command line support would be awesome, and a built in automation feature would be even better. Just let XenonMKV sit in the tray as a process, or even make it a windows service, and convert any new files dropped into certain folder(s), putting the results in another defined folder(s). Would make my life much easier. (and soooo many other people's too)