My official guess is AMD 7xxx series cards.
If they add an 8 pin plug, we'll see 7970 as top. If they stick with the underwhelming Dual 6 pins arrangement, we'll see 7950. But as I think about this, Apple usually likes to offer the TOP of a particular single GPU range. There are more hints of 7xxx cards in the drivers then hints of Kepler (GTX6xx) but this means very little.
IIRC, both the 4870 and 5870 had special driver packages that came out with the Mac they got introduced in. This meant that until you got those special OS builds, even if you had the card it was no go.
I have tested 7970 and GTX680 in every OS build released and I can tell you there is no support for them. I was going to rule GTX6xx out completely because there is no low to mid level GTX6xx card out for entry level, but then I got an email today from a friend at Nvidia pointing out their nifty new GT 640. This would make a perfectly fine "base" card for 6,1.
http://www.evga.com/articles/00686/#Dual
So with new cards we will either get a 10.7.4 "Special 6,1 Mac Pro Version" or 10.7.5 or 10.8 GM and it will add support for whichever cards they go with.
The fact that Nvidia has been going above and beyond to keep current Mac OSX drivers available bodes well for new cards being AMD. I can't picture Nvidia poking & pestering Apple with support for unsupported cards if they were about to launch a new series of cards with them.
Another reason I think AMD more likely is that we typically get cards MONTHS after they are released, usually right before EOL of "Toc" update. GTX6xx cards just came out in late March, not the usual amount of time needed to solidify drivers by Apple's glacial standards.
So my best guess is 7xxx series AMD with quite likely a Quadro (or other "Pro" card once available) from Nvidia a little later on.
The requirement for ThunderBolt tosses a really interesting set of issues in. Apple may take advantage of this and make new GPUs not work in older Macs. (They love to do this) Since there is no TB support on 1,1 through 5,1 LogicBoard there is no reason to expect adding a TB GPU would magically add this support.
It is even LESS likely that they would manufacture 2 different versions of the cards so that those of us running pre-6,1 could have them too.
I doubt very much that they will use 6xxx AMD or GTX5xx cards as they are all PCIE 2.0 and it is almost assured that Mac Pro 6,1 will have PCIE 3.0. They can't tout "New PCIE 3.0 throughput on your 6,1....someday when we offer PCIE 3.0 GPUs...for now enjoy a nostalgic look back to PCIE 2.0 with last season's cards" as a sales point.
So, my take on tea leaves:
AMD 7xxx cards most likely with 7570 or 7670 or 7770 as base with either 7950 or 7970 as top.
Slightly less likely is:
Green team with GT 640 as base and GTX680 as top IS a 2nd possible option. The GTX680 would be an IDEAL Mac card, although it's intentionally crippled GPU performance means that GTX570/580 may still be "the" cards for CUDA/OpenCl until Pro level cards appear.
Going to be a crazy day on Monday. If they announce that the new machines are already available at Apple Stores I will be heading to The Grove and getting whatever they have.
Keep in mind that in the past, they announced 5870 but they weren't available for many weeks after. And getting one as a separate purchase took months as I recall. So we may only be able to get our hands on the entry level cards for awhile.
If I close my eyes, can I make it be Monday?
