The iPhone (3GS, 4, 4S, etc) often records video upside-down but then includes metadata about the rotation inside the MOV container.
However, many applications (XBMC, VLC, Windows Media Player) do not understand this rotation metadata and so the videos play upside-down.
Is it possible to permanently rotate these videos and remove/ignore the rotation flag?

-vf rotate=1option to achieve the same. The output options will need tweaking though, to get decent quality. – slhck Dec 27 '11 at 19:04