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