MKVtoolnix

MKVtoolnix 5.6

Free
MKVToolNix is a set of tools to create, alter and inspect Matroska files
4.1  (94 votes)
6.6
12.0.0 (See all)

27 May 2012: Released v5.6.0. It fixes a couple of important issues with the new --split parts: functionality. Other bugs were fixed as well. A Polish translation of the programs has been added as well as a Spanish translation of mmg’s guide.
Here are the usual links: the home page, the source code and the Windows installer and 7zip archive.
All of the binaries that are already available.

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