Some of the main differences:
GE has top feed fuel injectors/rail, GTE has side feed
GE has a 6 stud exhaust flange, GTE has 7 stud, later ones had 8 (or was it 9?)
The cams appear to be the same; I measured with a cheap plastic venier caliper that sits in toolbox, but I'll probably need something more accurate to find if there's any difference. Anyway they both appear to be around 7.8-8.0mm lift, on both intake and exhaust; in fact the GE has two intake cams in it for some reason (both have slots for the distributor)
Anyway, I've taken some pictures of the ports for the sake of comparison.
Exhaust side, first is 3S-GE, I put the 3S-GTE exhaust gasket on to make comparison easier:

and the 3S-GTE:

Inlet side, 3S-GE first. For some reason this already had a T-VIS gasket on it, so you can clearly see the difference in the port size:

and the 3S-GTE T-VIS head:

And stolen from Richard Doig's website, here's a Gen 3 inlet side:

Close up of the inlet ports, 3S-GE first. You can see this is a fairly uniform size right the way down:

And the 3S-GTE one, this tapers quite severely from the large size required by the T-VIS system, down to roughly the same size as the GE head:

And finally, here's a shot of the combustion chambers. The valves appear to be the same size, but I'll measure them later. 3S-GE first:

and 3S-GTE:

Notice how the 3S-GTE is much whiter on the exhaust valves? I'm guessing this is due to the extra heat created by the turbo engine.