For whatever reason every time I have shot a portrait mode video with my Motorola Atrix cellphone. Today the issue came up again and here is the command I finally used with acceptable success.

ffmpeg -i 2012-03-16_15-12-41_472.mp4 -vcodec libx264 -preset medium -crf 24 \
 -threads 0 -vf transpose=1 -acodec copy output.mkv

It isn't perfect, but, it is good enough, I hope this helps