MKVtoolnix is a set of tools to create, alter, split, join and inspect Matroska files(mkv). Command line tools but mkvmergeGUI/mmg.exe frontend is included. Use MKVExtractGUI-2 to extract/demultiplex mkv video and audio files.

This i a great tool for Anime Music Video makers/editors that require to work with .mkv files. So why convert a file when you can just extract video, audio or subtitles….all in a different file.

Easy to use tool for multiplexing Matroska streams with a Windows native GUI. Flexible, logically organized, and supports almost all source formats well. De facto standard.

The existance of this GUI program is a major reason for the success of MKV. Creating files this format is so much easier and overall more reliable than working with AVIs or MPEG Programs, let alone MP4s.
During its development, the author has made a number significant changes to the format of files written by MkvToolNix, such as the format of MPEG sequence headers, stream header compression, and presence of a seek element, which might not be immediately apparent. Some of these changes had since been reverted. I would excercise caution before upgrading to a new version, thoroughly read the changelog and test that the output files are working on all devices and players they are intended to work, and that no unexpected artifacts appear and seeking works.