I've been trying to find away to get my .mkv and .ogg files to play on my zune and have the subtitles actually work and come up. I have found a almost bullet proof way of doing so,
I use "AlltoAvi", freeware and can be downloaded from afterdawn, and open the .mkv file. You have to tell it to look at all file and not video files because it will not open .mkv be default.
I tell it to convert the file, and it opens a pop up that gives me special options. These special options will not come up if you pick quick conversation. It gives my a choice of video size, video quality and video frame rate, and audio options. I choose excellent everything. There is also a choice for subtitles if there is subtitles in the mkv or ogg file. I pick the correct subtitle choice, English in my case, and select ok, and then convert.
The Avi files comes out about the same files size as the original file, and takes about 20 minutes for a 400mb .mkv file. Depending on the type of .mkv file, the converted AVI will be able to go right onto the zune or you may have to use an avi converter. I use the Jodix Ipod converter to some of the avi files into zune files. I am under the thought that if the .mkv or ogg file using the h264 or divx compression that you have to use the Jovix Ipod Convertor.
Both Programs support batch file conversions, so I batch convert a few gigs of video overnight and I can put them on my zune in the morning.
Just thought this might help someone because it took me about two weeks of trying programs and reading to figure this out. This is also great because both programs are freeware.
