In case it helps anyone, here is the bash script I used to batch convert the files on my ubuntu machine. I compiled ffmpeg from svn tonight.
Code:
#!/bin/bash
for i in $( ls *.mp4 ); do
ffmpeg -i $i -ar 22050 -ab 56k -aspect 4:3 -b 200k -f flv -s 320x240 -acodec libmp3lame -ac 1 $i.flv
mv $i.flv ${i%.mp4}.flv
done