mencoder

mencoder input.avi -o output.flv \
     -of lavf \
     -oac mp3lame \
     -ovc lavc \
     -lavcopts vcodec=flv

More options (from mplayer/mencoder man page)

mencoder input.avi -o output.flv \
     -of lavf \
     -oac mp3lame -lameopts abr:br=56 -srate 22050 \
     -ovc lavc \
     -lavcopts vcodec=flv:vbitrate=500:mbd=2:mv0:trell:v4mv:cbp:last_pred=3

• converts Intel Indeo 5 AVI (contrary to ffmpeg)
• to resize the video, add

-vf scale=<width>:<height>