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Everyone always mentions free encoders like MediaCoder. These give you poor FLVs because the codec they support is very old, dating back to Flash 6 days. This is the same for any app that uses FFmpeg for encoding.
If you want decent FLVs you need to pay for an encoder - at least for now, until and IF Google makes the codecs open source. Flix from On2 (now owned by Google) is one such program. Look for an encoder that supports VP6. A video encoded with VP6 will play back on Flash 8 or later. Nearly all FLV players require at least Flash 8, and the latest latest versions of the top-end players (JW Player, Flowplayer) require Flash 9 or above. VP6 videos have much better resolution than the older Sorenson Spark/VP3 vids.
I don't recall if the $40 Standard version of Flix does things in batches, but it might.
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