MKVToolNix is a small collection of tools (mkvmerge, mkvinfo, mkvextract, mkvpropedit and mmg) with a GUI that allows you to manipulate Matroska (MKV) files in several ways. You can use MKVToolNix to create, split, edit, mux, demux, merge, extract or inspect Matroska files. The program will also work with other video formats (AVI, MPEG, MP4, MPEG, Ogg/OGM, RealVideo, MPEG1/2, h264/AVC, Dirac, VC1) including some video codecs (such as VP9 video codec support - reading from IVF/Matroska/WebM files, extract to IVF files). Audio formats (AAC, FLAC, MP2, MP3, (E)AC3, DTS/DTS-HD, Vorbis, RealAudio) and also most subtitle formats (SRT, PGS/SUP, VobSub, ASS, SSA, etc.). MKVToolNix is a cross-platform application that will work on Windows (both 32 and 64-bit versions), Mac OS X and Linux.
Thanks to flash13 & zoran for the update.