encoding to matroska files is to be supported.  This doc describes required steps.

Matroska is an advanced open video wrapper.  It can contain video and audio
streams along with metadata.  Playback support is adequate on multiple 
platforms, and development is only progressing.

Matroska reencoding is supported in Jivo for the main reason of metadata
unification, which means that it is possible to have the metadata imbedded
in the video file.  The primary advantage of unified metadata is seen on
data interchange and data restoration.  When a mkv file with markup is found
the markup can possibly be extracted and integrated into a search system.  Say
for example that a friend sends you some Puppets Who Kill episodes that have
been recorded and says that his favourite is the one where the preacher kills Buttons for sleeping with his wife.  With metadata it would be possible for
the system to detect addition of files to the library and then the mkv metadata
could be read and the files could be searched for 'preacher Buttons', which
would show the episode.  There are many other benefits, such as increasing
resolution of show information (addition/modification of metadata as a file
drifts, etc).  

There are Jivo recorder plugins to encode to mkv and plugins to update
metadata with airing info (airing, programme, channel, cast, etc).  Further
integration is planned.

Eventually, imbedded and communally maintained metadata should lead to 
better accuracy in finding information across disparate networks.

links:
http://www.matroska.org/
http://www.bunkus.org/videotools/mkvtoolnix/
http://svn.matroska.org/viewsvn/trunk/JEBML/
http://www.cse.iitb.ac.in/~gautham_anil/projects/any2mkv/