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The best: Adobe Media Encoder
However, "Handbrake" (free) will take care of all your MP4 encoding, but I don't believe it does FLV. At least I've never noticed if it does.
If you're going to encode MP4, you can play those in a FLV player and bypass the FLV file. MP4 will give you better quality at a small file size. It's also stable, won't crash browsers and will play on iPhones.
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