I\'m looking to accomplish the best quality FLV with the lowest file size. After all, isn\'t that everyone\'s goal? These videos will be streamed if that makes any difference.>
I think the best solution to maximize the ratio quality/size is to scrap the "flv" encoding of ffmpeg altogether, and use H.264 instead.
I'm usually using handbrake to convert files to MP4/AAC, and then only use FFMPEG to remux the file into an FLV container.
ffmpeg -i input_file.mp4 -vcodec copy -acodec copy -y output_file.flv
There are also a lot of parameters for handbrake, some interesting presets can be found here: http://trac.handbrake.fr/wiki/BuiltInPresets