On one of the websites that I was building, I had Next-Gen Galleries and YouTube videos on the same page. In one instance, I would click on the image for the thickbox to appear and the YouTube video sat on top. The YouTube video was embedded as an iframe.
[html]<iframe height="360" frameborder="0" width="580" src="http://www.youtube.com/embed/odXK8yMCuwM?color1=234900&color2=4e9e00&border=0&fs=1&hl=en&autoplay=0&showinfo=0&iv_load_policy=3&showsearch=0&rel=1" title="YouTube video player"></iframe>[/html]
So in order to add the wmode property to the video, I added &wmode=Opaque to the end of the URL, so:
[html]<iframe height="360" frameborder="0" width="580" src="http://www.youtube.com/embed/odXK8yMCuwM?color1=234900&color2=4e9e00&border=0&fs=1&hl=en&autoplay=0&showinfo=0&iv_load_policy=3&showsearch=0&rel=1&wmode=Opaque" title="YouTube video player"></iframe>[/html]
Then I was able to view my lightbox/thickbox with no issues.