I had quite some trouble setting up the JW player correctly. So once I got it right I wanted to write down what I did to help anyone who has the same problem as I had.

(I'm not sure where to place this. I thought it would fit in the SWF Tools documentation, http://drupal.org/node/141706, but I don't feel like I can place something there... So feel free to move it anywhere you want.)

- You need to have the Video and SWFTools modules installed.
- In the Video module configuration set 'SWF Tools' as 'Flash Player'.
- In your display settings of your video field, select 'SWF Tools' (with or without link/playlist)
- Get the JW player from http://www.longtailvideo.com/players/ and upload it to 'sites/all/modules/swftools/shared' (so you get 'sites/all/modules/swftools/shared/flash_media_player/player.swf'). (or any other path you configured as the 'Default flash player path' on your SWFTools > File handling page)
- After uploading the player clear your caches to force the SWFTools module to look for the player;
now the JW player should be selectable on the SWFTools > File handling page. Do so and save you configuration.
- Your video files should now be displayed in the JW player.

(If you can select the player but instead of seeing the player get the message that 'You are missing some Flash content' you might want to check that your player.swf file has UNIX rights that allows reading by others (chmod at least 004))

(I used Video 6.x-4.2 | SWFTools 6.x-2.5 | JW mediaplayer 5.7 (JW mediaplayer 4.0 also tested and worked))

See also #2 at #797730: JW player not found when upgrading 6.x-2.5 to 6.x-3.0-beta4