One of the beauties of the the JW Player 5 is it's ability to embed MP4 videos via HTML5 video tag when the visitor doesn't have Flash or is using an iPhone or iPad... Currently I'm using SWFTools with JWPlayer5 along with the Video Module with Zencoder MP4 file conversion and Amazon S3 storage. It's too perfect and needed no server config or installations to achieve!! The only issue I had was testing it on iPhone where it showed the "No Flash player found" type message. I couldn't stop there, so I created a module based on the SWFObject2 submodule. This gives you the ability to choose the JW Embedder method that comes with the JW Player 5. I attached it if anyone needs it.
NOTE: It's working perfectly with JW 5.6, and havn't tested it with JW 5.7 yet. Just make sure the jwplayer.js file is inside the sites/all/libraries/mediaplayer-5 directory next to the player.swf file.
It would be great to have the JW Embedder option shipped with the SWFTools 6-x.3. Otherwise were not using the JW Player to its full ability. The JW docs recommends using it over anything else.