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If you care about the best quality I would recommend a desktop app that supports the ON2 VP6 codec where you can fine tune the controls like Sorenson Squeeze or Flix Pro. Since I am an original content creator I have never server side apps but I suppose that they have their use if you already have hundreds or thousands of pre-existing files already on the server that you want to convert and you are willing to live with the limitattions of the server side freeware apps. It's not quite the same as using the very best apps and codecs and fine tuning them to get the very best quality possible however.
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