I've been using this line on MobileBoner.com to encode flv's to mpeg4's in .mov containers so that they are able to stream to the iPhone/iPod touch
ffmpeg -y -acodec libfaac -ab 128kb -s 320x240 -vcodec mpeg4 -qscale 5 -mbd 2 -flags +4mv+trell -aic 2 -cmp 2 -subcmp 2 output.mov -i input.flv
It works aiight, but only seems to stream to the iPhone.