My brother mocked my use of ffmpeg to create flash video as I did a couple of days ago. He sent me this set of command line options for the Swiss Army knife of video encoders: mencoder. I went ahead and encoded the classic civil defense film "Duck and Cover", and then used the flvtool2 to add indexing.
Here is the result:
Here is a little shell script that shows the options. I used mencoder as installed fresh from a new Fiesty Fawn Ubuntu installation. If you install rubygems, you can then type "sudo gem install flvtool2" to get flvtool2 installed (it is in /var/lib/gems/1.8/bin/flvtool2, which is not in my path, but it's there), and it seems to work well too.
Anyway, Kevin wanted me to test it, and it seems to work.