Best method to upload / link to multimedia files in D6?
Have a look at ShadowBox, it supports a lot of formats and the FileField module which I think is essential for your set up:


  Media extensions supported:
  - Images (png, jpg, jpeg, gif, bmp)
  - Video (avi, mpg, mpeg)
  - Quicktime (dv, mov, moov, movie, mp4)
  - Windows Media Player (asf, wm, wmv)
  - Flash (swf, flv)
  - IFrame (asp, aspx, cgi, cfm, htm, html, pdf, pl, php*, phtml, rb, rhtml, shtml, txt, vbs)


Source: Comparison of Lightbox-type modules.

There's algo the Lightbox2 module with is aroung since a long time and have quite a big installed base.