I'm well aware of the complications, however, I've found a lot of it comes down to priming your audience. I used subtle orbiting motions, slow transitions and reference grids to let the audience see where the depth was at all times. I haven't tried adding real shadows or SSAO, but it would only enhance this. There's also 3d displays to consider.
I think part of the problem is that we haven't had good tools to do this with. My mental sketchpad is in 3d, mathbox is what it looks like.
If you are trying to understand three-dimensional functions, it makes sense to view them in 3D. I was just pointing out that in the domain of information visualization (separate from math and scientific visualization), 2D is generally preferred for perceptual reasons.
Indeed, thank you! Hugs all around. :) You made the argument that D3 doesn't do 3D because of the DOM, and I just wanted to clarify that while this is mostly true (caveat custom elements such as X3DOM), the reason is perceptual as much as technical.