Make sure you have:

deb http://www.debian-multimedia.org unstable main

in your sources.list. Then sudo apt-get update && sudo apt-get install mencoder.

Finally, run something like:

mencoder -vf rotate=1 -o rotated.avi -oac copy -ovc lavc /mnt/sd/dcim/101canon/mvi_3099.avi

If you take the video from upside down:

mencoder -vf mirror,flip -o flip-mirror.avi -oac copy -ovc lavc /mnt/sd/dcim/101canon/mvi_3104.avi
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