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180 degree rotating/flipping can be very easily implemented in
ffmpeg. I did it in the do_video_out function by hacking the
pixel format conversion part of the code in it : I first convert
the picture to RGB format, flip/rotate it in memory (array ops)
and convert it back to the encoder pixel format.

90 degree seems to be problematic since you need to modify
the frame size info for the target stream. Since not all codec
(mpeg 2 profiles have fixed rsolutions ) it may impact on
codecs.

I am interested in the 90 degree conversion for embedded
device applications.