ffmpeg on my server works great and is fast but i can get 30% smaller file sizes with video charge and still look as good. using h263 codec (i think)
i haven't had time to update the server one yet as its not that important, just as easy for me to do it local here and upload it to my script
see quality here if interested;
http://www.bvbucks.com/flash/?affil_id=1352409