MKVToolnix is described as 'set of tools to create, alter and inspect Matroska files under Linux, other Unices and Windows. They do for Matroska what the OGMtools do for the OGM format and then some. The latest builds now have the ability to create WebM compliant Files' and is a very popular app in the video & movies category. There are more than 25 alternatives to MKVToolnix for a variety of platforms, including Windows, Mac, Linux, Android and Android Tablet. The best alternative is FFmpeg, which is both free and Open Source. Other great apps like MKVToolnix are MP4Tools, MKVExtractGUI, Video Transcoder and gMKVExtractGUI.
MKVToolnix is mainly a Video Converter but alternatives to it may also be Video Editors or Audio Converters. Filter by these if you want a narrower list of alternatives or looking for a specific functionality of MKVToolnix.
FFmpeg is the leading multimedia framework, able to decode, encode, transcode, mux, demux, stream, filter and play pretty much anything that humans and machines have created. It supports the most obscure ancient formats up to the cutting edge.
Almost everyone thinks FFmpeg is a great alternative to MKVToolnix.
Video Transcoder is an application which uses the open source program ffmpeg to transcode video files from one format to another. By selecting the video to process, details for the video are provided and the desired settings can be configured.
Subler is a Mac OS X application that opens media containers, allows you to add or remove media tracks inside them, and then saves them out again. In the specialized language of the video world, Subler is a “transcoder” or “demuxer” depending on how you use it.
Voukoder is system wide video- and audio encoding service for Windows that improves your media encoding experience. It supports various encoders (both CPU and GPU based) and also provides a set of post processing filters.