mkclean is a command line tool to clean and optimize Matroska (.mkv / .mka / .mks / .mk3d) and WebM (.webm / .weba) files that have already been muxed. It reorders the elements with the Cues at the front, so your Matroska files are ready to be streamed efficiently over the web. It also removes elements not found in the Matroska specs and the extra Meta Seek list of Clusters that some program add to their file. It can also optionally remux the Cluster blocks to start each boundary with a keyframe and the matching audio/subtitle blocks for that keyframe.

Authors Site (support): http://www.matroska.org/downloads/mkclean.html
Download (Mac): http://sourceforge.net/projects/matroska/files/mkclean/mkclean-osx-0.8.6.tar.bz2/download
Download (Linux): http://sourceforge.net/projects/matroska/files/mkclean/mkclean-0.8.6.tar.bz2/download
Download (Windows): http://sourceforge.net/projects/matroska/files/mkclean/mkclean-win32.v0.8.6.zip/download

mkvalidator is a simple command line tool to verify Matroska and WebM files for spec conformance. It checks the various bogus or missing key elements against the EBML DocType version of the file and reports the errors/warnings in the command line.

Authors Site (support): http://www.matroska.org/downloads/mkvalidator.html
Download (Mac): http://sourceforge.net/projects/matroska/files/mkvalidator/mkvalidator-osx-0.3.7.tar.bz2/download
Download (Linux): http://sourceforge.net/projects/matroska/files/mkvalidator/mkvalidator-0.3.7.tar.bz2/download
Download (Windows): http://sourceforge.net/projects/matroska/files/mkvalidator/mkvalidator-win32.v0.3.7.zip/download