Alright it looks as if .mkv files will play back using the newest version of nitotv. With a hacked version of Apple TV running NitoTV it will use the best option to play all new formats. It uses mplayer to play .mkv files, and will be able to have Dolby Digital have pass though?
Mplayer also handles ts-video folders, .as well as Divix/xvid avi.