I've only seen it in anime as well. VLC and Mplayer have worked great for me. But when I started using front row, it had to be quicktime compatible. So I used this to extract the avi's or whatever is in there. You get to pick which audio/subtitle track you want in the mix, and pops the avi's right out of MKV. Maybe it'll be of some use.
http://www.macupdate.com/info.php/id/24872/mokgvm2dvd
P.S. Does quicktime allow for soft subtitles??
If you have Perian installed to play MKVs in QuickTime, yes. There's also some support in QT for MP4's "TTXT" soft-subtitles, but there's no good way to create them or mux them into MP4's in OS X. I played around with it once, but it's kind of a bitch. I think it might get easier as "closed captioning" on iTunes video material gets more common though. In fact, I'm wondering if that's what they're using to accomplish that at the moment. Haven't bought anything that's captioned/subtitled off iTunes recently, so I'm not sure.
EDIT: Perian (or QuickTime) also currently has a bug where MKVs with soft-subtitles will play back with their embedded fonts displaying correctly when you're just playing them, but if you try to export to another format, all formatting disappears. It's bizarre.