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A server side script like ffmpeg will never be able to match the quality and flexibility of a dedicated video encoding app like Videocharge or Sorenson, although it may come close enough for your purposes. For one, ffmpeg may not use the latest codecs or latest versions of the codecs. For example, with Flash the preferred codec is On2VP6. I am not sure if ffmpeg takes advantage of that, or if it can do mp4 either. But more importantly, if you know what you are doing, when you manually do video encoding, you can tweak the output with a custom bitrate, constant or variable and take advantage of special filters to make the encoded video look better. I personally often use a slight sharpness & brightness and contrast filter on my videos to make them look a little more pleasing to the eye. As far as I am concerned, if you have original masters and high quality footage, you should do the encoding yourself on your own workstations. The only reason to use ffmpeg is if you have hundreds or thousands of pre-existing encoded vids on your server already that you don't have the source tapes for and you want to convert them from one end user format to another without downloading them and re-uploading.
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