Update: Use H.264 and AAC in mp4. It’s more portable (the file can be played in more places) and the quality is much better. See my FFmpeg x264 encoding guide.

This page details how to encode flash video for embedded flash playback. You may want to resize the video but considering the inputs I was using, I didn’t.

Input: 320×240 15fps MJPEG + unsigned 8-bit 11024Hz mono PCM in AVI [Canon PowerShot A60]
Input: 320×240 15fps MJPEG + unsigned 8-bit 7875Hz mono PCM in mov [Nikon Coolpix L3]

FFmpeg

ffmpeg -i input -ar 22050 -acodec libmp3lame -ab 96k -vcodec flv -b 300k -g 150 -cmp 2 -subcmp 2 -mbd 2 -flags +aic+cbp+mv0+mv4+trell outfile.flv

Thankfully there will soon be a GPL VP6 encoder available which should allow for greatly improved open source flash video quality. And some even better news – Adobe have added H.264 and AAC in MP4 playback support to their Flash Player in current betas available from the Adobe labs website!!!