MKVToolNix is a 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.
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.