But why the hell would you want anything in the Matroska format?
Just saying...
Anyway, I'm a VLC user too. But mostly because I'm too lazy to learn how to use something more advanced.
I probably should get around to learning, though--
By the way, I'm assuming you can do this using the method you just mentioned Ynot, but how would I go about converting a .flv (Flash video) to a .3gp (Cell phone video). I don't know what video codec .3gp uses, but I know it uses AAC audio.
Anyway.