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If you want to retain some quality avoid FFmpeg, or any software (like Moyea) based on it. FFmpeg only supports a very old FLV codec (called Sorenson Spark). You get much better quality, with smaller file size, by using the FLV VP6 codec.
The encoder in Adobe Flash 8 Professional and above comes with the VP6 encoder, or you can purchase a stand-alone one from On2. If you want precise control you have to get the Pro version, but there are settings in the cheapo Standard version that allow more-or-less pass-through bitrate quality, framerate, and sizing.
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