Lower quality of a video?

I've got a few mkv files that I need to lower the quality of because I play them on my Wii via Wii Media Center and it just can't handle them. Is there any software available for FreeBSD that will do this?
 
There are (good) GUI options too:
multimedia/gmencoder
multimedia/arista
multimedia/handbrake

Maybe have some more, but for FreeBSD I don't know.

Cheers.
 
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