Matroska had a Stereo flag for a long time. Stereo 3D has always been an early goal for Matroska but we lacked the use and devices/real life examples to test. Now Stereo 3D is becoming a reality in the living room on computers and even more in movie theatres. After a month of back and forth work (and a visit of the IBC Show 2010) we finally have a stable solution that should fit all the known cases.
Stereo 3D in Matroska can be handled with either a single track using codecs like MVC or side by side like most current 3D broadcasts. This is defined by the updated StereoMode field. Stereo 3D can also be handled by combining 2 or more tracks together. This is done by using the newly added TrackOperation field. This field defines a virtual track that is created by combining other tracks for various 3D planes. It may also be used for other virtual tracks, like combining 2 subtitle tracks into one (like it is the case with DVBSUB).
Now we need the tools to create and play such files. mkvmerge should be updated soon to support this and VLC to handle the playback. So stay tuned for more announcements.