IMHO, JWPlayer is better for novice users and/or experience people who wants to use a very good yet basic player (I mean without plugins and further customization). Flowplayer is better for those looking for way more features, more power and less server load on multiple video player environments. Both are very good and I use them both on a regular basis, depending on the project I'll use one or the other, although as of late I'm leaning more and more to Flowplayer
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