MKVtoolnix is a suite of tools for creation and edition of MKV files. The application is command-line based, but the Windows versions have a GUI called MKVmerge GUI. It is a graphical interface for the command-line application.
It has an unbelievable list of supported input formats. Although this application is evidently more fit for experienced users, anyone can use it to carry out rather basic tasks. For example, when you add a video file into the GUI, MKVtoolnix will return how many tracks the file contains. I added a sample for an XVID clip, and it returned an XVID video track and an AC3 audio track. When you are ready to convert the files to MKV, simply click on Start muxing, at the bottom of the page.
At the bottom of the GUI, you will see three tabs with different options. There are options for subtitles, audio, splitting the video file and also format-specific options. In short, MKVtoolnix has a lot to offer in terms of functionality, but one has to know about video files to really appreciate what this application can do.