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Try avidemux. It's a frontend for transcode and some other tools and it has support for x264 output. Should be fairly easy to do what you want, as long as you know what the output parameters are supposed to be.
I'm not 100% sure it can handle .mkv input though. But if mplayer can play the file, then it's likely. At the very least you should be able to convert the file with mencoder if it does. You can also use mplayer as an input module for transcode if you want to use it directly instead of through avidemux (transcode is much more flexible and powerful via cli).
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