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Here I try to add links to applications that have some relationship to MKVToolNix – e.g. programs that rely on or include mkvmerge itself. I haven't tested all of those myself, but you should given them a try anyway if they fit your needs.

If you're the author of an application that is not listed here and think that it should or if you know such an application then please let me know and I'll include a link and a description.

GUIs and batch operations

• MKV Muxing Batch GUI: app for muxing (merging) videos with [subtitles,audios,chapters,attachments] with many options
• bulk-mkv-muxer: a multi-threaded tool for batch-muxing of files into Matroska files
• MKVmergeBatcher: Windows GUI application for batch muxing with mkvmerge.exe
• MKVToolNix Batch Tool: A batch video and subtitle processing program to help you add (merge) or remove subtitles from your video library. Allows you to process a directory, and/or all of its subdirectories, in a single batch.
• gMKVExtractGUI: a GUI for mkvextract supporting its full range of features. Runs on Windows and Linux.
• MKVcleaver: MKVcleaver is a tool for batch extraction of data from MKV files. It is similar to mkvextractGUI in functionality, but allows loading of many files. There's also a forum post on doom9 about it.
• JMkvpropedit: a batch GUI for mkvpropedit written in Java
• MkTags: a simple Perl application that lets you edit the tags in a Matroska file. It can be used with WebM files as well, since this format is based on a profile of Matroska. It supports most of what’s in the official tag specifications.
• docker-mkvtoolnix: a Docker container for MKVToolNix. The GUI of the application is accessed through a modern web browser (no installation or configuration needed on the client side) or via any VNC client.

Ripping DVDs/BluRays into Matroska

• iso2mkv: a versatile convertor from DVD to XviD/vorbis MKV on top of MPlayer/MEncoder
• OGMRip: an application and a set of libraries for ripping and encoding DVD into AVI, OGM or Matroska files using a wide variety of codecs. It relies on mplayer, mencoder, ogmtools, oggenc and lame to perform its tasks. The GUI features a clean HIG-compliant GNOME 2 interface and tries to minimize as much as possible esoteric settings.
• Tuxrip: a Linux bash script for ripping and encoding DVD titles in mpeg4 format (DivX, XviD, FFmpeg libavcodec). It features per title or full DVD ripping, audio extraction and encoding, support for multi-audio tracks, 2-pass video compression for a given file size and quality, compressibility testing for optimal quality and resolution determination, support for codec options, audio/video synchronization, CD burning, and automatic computer shutdown.

Converting Matroska files into other files

• mkvdts2ac3: a bash script which can be used for converting the DTS in Matroska (MKV) files to AC3. It provides you with a healthy set of options for controlling the resulting file.