By default, the Drupal Lightbox2 module supports the flvPlayer flash movie player, which is not Open Source. However, Drupal has a 100% Open Source video player called Flashy. Here's a quick method of overriding Lightbox's setup to use Flashy instead of flvPlayer.
Assumptions: This article assumes that you already have Lightbox2 configured, and you already have fields configured to use Lightbox2's video support. All we are doing here is swapping Flashy in for flvPlayer.