FFmpeg command to rotate an MP4 file by 90º

With the current version pulled from SVN, you can rotate video using -vf "transpose=1".
Here's an example:

ffmpeg -vf "transpose=1" -i input.mp4 output.mp4

docs + options for transpose command are here

(here's how I built ffmpeg in case this helps)

svn checkout svn://svn.ffmpeg.org/ffmpeg/trunk ffmpeg
cd ffmpeg
./configure --enable-shared  --disable-mmx --arch=x86_64
make
sudo make install

Maybe it should be configured with --enable-vfilters before compilation? BTW, mencoder does the job well, but you'll have to reencode the video:

mencoder -oac copy -ovc lavc -vf rotate=1 original.mp4 -o 90_CW_rotated.mp4 mencoder -oac copy -ovc lavc -vf rotate=2 original.mp4 -o 90_CCW_rotated.mp4