Tan sencillo como:

For nokia n80
ffmpeg -i "$1" -ar 16000 -ac 1 -acodec aac -vcodec mpeg4 -s 352x288 -r 24 -b 350 -ab 32 "$1.3gp"

Nokia s60
ffmpeg -i movie.avi -s 172x144 -r 10 -ac 1 -b 48 -ab 12 movie.3gp

Nokia NSeries
ffmpeg -i movie.avi -f mp4 -vcodec mpeg4 -b 250000 -r 15 -s 320x176 -acodec aac -ar 24000 -ab 64 -ac 2 movie.mp4

Nokia 3250, 5500, E50, E62
ffmpeg -i movie.avi -f 3gp -vcodec 3gp -b 100000 -s 320x176 -r 12 -acodec aac -ar 8000 -ab 16 -ac 1 movie.3gp

For Ipod
ffmpeg -vcodec xvid -i input.avi -b 375 -qmax 10 -bufsize 8192 -g 300 -acodec aac -ab 96 -ac 2 -s 320×192 output.mp4

Ipod (fullscreen)
ffmpeg -i in.avi -f mp4 -vcodec mpeg4 -maxrate 1000 -b 700 -qmin 3 -qmax 5 -bufsize 4096 -g 300 -acodec aac -ab 192 -s 320x240 -aspect 4:3 out.mp4

Ipod (widescreen)
ffmpeg -i in.avi -f mp4 -vcodec mpeg4 -maxrate 1000 -b 700 -qmin 3 -qmax 5 -bufsize 4096 -g 300 -acodec aac -ab 192 -s 320x180 -aspect 16:9 out.mp4

Yo para mi e61i uso: ffmpeg -i movie.avi -f mp4 -vcodec mpeg4 -b 250000 -r 15 -s 320x176 -acodec aac -ar 24000 -ab 64 -ac 2 movie.mp4

Desde: http://apairudin.blogspot.com/2008_01_01_archive.html
Y: http://blogs.s60.com/s60multimedia/2006/11/video_transcoding_using_ffmpeg.html