Smart Converter Pro is dead simple, and depending on the target format will automatically convert or extract the format in the .mkv to the correct format. Say you have a .mkv that encapsulates mp4 video and want the target platform to be Playstation 3. It will simply extract the mp4 (and convert the audio if necessary). I highly recommend this for dead simple MKV conversions. Now if you need to do more advanced transcoding, like say target a file size, etc... This isn't the program to use.
http://www.shedworx.com/smart-converter-pro
I use this as well for simple conversions - the paid version is much better and for the average home user it provides all the functionality you could ask for!