• Is there any interface for lighting the surfaces?

Nope. CSS3D doesn't have such feature. It's true that it can be implemented but it's a hack...

• The molecule example - why are some images "billboarded" (the atoms) and some not (the bonds)?

Try to billboard the bonds. You'll see that it can't be done :)

• Is there any API in three for two sided v. one sided planes?

Not yet.

• how much of three.js in general carries through with css3 and how much does not?

The CSS3DRenderer basically reuses the scene graph (compute matrices) but can't handle geometries nor materials.

Just for reference if anyone finds this post:
backface-visibility: hidden; can be used in css to hide dom elements pointing away to mimic one sided faces.

This also works with the periodic table example.