Write out the JPEG frames:
avconv -i WHOOPS.AVI -c:v copy -bsf:v mjpeg2jpeg frame_%d.jpg
Rotate them losslessly:
exiftran -i -2 frame*.jpg
Reassemble the frames and grab the audio from the original file to create a new complete file:
avconv -framerate 29.97 -i frame_%d.jpg -i WHOOPS.AVI -codec copy /
-map 0:v -map 1:a ROTATED.AVI
Update: When this was originally written, Ubuntu was using the avconf fork of ffmpeg. These days, try replacing `avconv` in the commands above with `ffmpeg`.
