I have a series of video links. On each click, I want to open the video modaly. I thought of using internal divs for each video (hidden at page load) but then it didn't seem to be a good practice since I would need 5 div for each video's player. So, I thought of preparing the player in external file, pass the variables with PHP and play the video file. My player is JW and the videos are FLV.

I can't find a solution that can do this though I tried simplemodal, thickbox etc...any suggestions?

Your simplemodal/thickbox approach should work but you should be able to achieve it with just one modal div (plus its contents) in total. This should work providing you want just one video to play at a time.

Accommodate the various videos with DHTML/DOM scripting (javascript). I can't help with the specifics because I don't know JW or FLV. Try searching the web. I'm sure someone has done it before. Here possibly.