Eu instalei o ffmpeg, libfaad, libfaac e x264 e tenho usado este comando
ffmpeg -i "file.avi" -acodec libfaac -ab 128k -s 640x480 -vcodec libx264 -vpre hq -vpre ipod640 -threads 0 -f ipod "file.m4v"
Eu construo o ffmpeg dessa maneira
svn checkout svn://svn.ffmpeg.org/ffmpeg/trunk ffmpeg
cd ffmpeg
./configure --enable-gpl --enable-version3 --enable-nonfree --enable-postproc --enable-pthreads --enable-libfaac --enable-libfaad --enable-libmp3lame --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libtheora --enable-libx264 --enable-libxvid --enable-x11grab
make all