I'd say it's 3D in the sense that it's a height map rather than a cross section. (We've been able to see cross-sectional images of bonds for some time using transmission electron microscopy, I think). It's not a full three-dimensional structure though, and it'd only work on flattish molecules like this.

It should be noted that this sort of resolution has been attainable for some time using scanning tunneling microscopy, but I'm pretty sure this is a first for atomic force microscopy. STM doesn't give you a very good image of bonds -- in fact bonds are generally the thing you _don't_ see, since STM works by pulling electrons in/out and bonds are stable places where electrons really don't want to come out of or go into. AFM, on the other hand, shows bonds very nicely.

You can sorta make out where the aromatic rings are. I'm not sure why it's so bright at the ends -- any organic chemists out there who can explain that?

about the brightness at the ends - I'm pretty sure that is due to the fact that this is a pi-conjugated system; that is, the pi-bonded electrons can jump around the whole molecule. This, together with the fact that the molecule is finite in size, means that the pi electrons are confined to a rectangle of lower potential energy, and when you solve the quantum mechanics (similarly to the quantum harmonic oscillator) you'll find higher electron density at the edges of the confining potential.

I'm totally willing to trust the word of someone called "graphene" on this one.

Those "clouds" are probability clouds. It means that the electron should be in the vicinity of the cloud at any given time.

Also, consider that an electron is 1/1000 the size of a proton.

actually, if you consider that afm is directly detecting charges, I guess we're talking about more than probability here - that picture ought to be a (rough) record of where the charges in that molecule were as the AFM needle passed over the molecule in that 20hr period

Electrons in an atom don't have a [specific] location. It's not a concept that exists for them. So, yes, it's a probability.

Despite the common image, electrons don't orbit the nucleus like planets around the sun. They sort of exist around the entire thing in all locations at the same time (in 3D, not in a ring, but a shell).