In this AMV the creator mixed scenes of the band playing from the real music video into the video with compositing. On Linux it is really easy to do this same effect with a high level of control, only down fall is you got to be able to visualize what you want, it's a good idea to think about this and try to draw it out or write it out on paper.
So here it is an a nutshell, we open a blank image in Inkscape and use black and white, then open that in say, OpenShot and select which color to make transparent. It is as easy as that, and with the help of key frames that image can be animated across the screen, like a moving window to the background layer of video.
Song: Best of You
Artist: Foo Fighters