we had four flatscreen monitors running DVD loops, six overhead transparencies on light boxes, and a whole mess of physical buttons lit from below. The great thing about this is we got the best of all worlds in that we had animations running on the consoles that we didn't have to matte, the controls were "practical" in that they were physical and the actors could interact with them by touch, and the overhead graphics are easy to replace in post if we want (in some cases we'd pull out the artwork and slap a green filter and diffusion in there to make an instant greenscreen.
The other benefit of having backlit art/buttons/lit screens is you get something that's difficult to achieve if you add them in post: interactive lighting. Note in the second pic that you can see the glow from the buttons on the hand of the actress just left of center.
The trickiest part is the holographic table projections, but so far NEO f/x is doing a bang-up job match moving that stuff, even when actors pass in front of it.