For those of you who want to convert from MKV and preserve subtitles, I just found this last night. It seems to work pretty good, I've only tried it on one though. It demuxes the mkv and remuxes everything, hardsubbing in the process.

It also seems like its hit or miss depending on your OS from what I've read. I'm using XP, and it converted the file ok, subtitles intact

Here's the link:
http://sentry23.googlepages.com/