A reasonable overview of what we’re likely to see by Chris Foresman at Ars Technica.
On page 2, because this article is so long that it needs to be split into two pages, Foresman notes the problem of what to do about sending DisplayPort over Thunderbolt:
The complicating issue is that Thunderbolt not only carries high-speed PCIe data, but must also carry DisplayPort video as well. On all other Macs, GPUs—whether integrated or discrete—are fixed. This makes it easy to pipe the DisplayPort output to the Thunderbolt port, which serves as both a high-speed interconnect as well as the connection for an external monitor. The Mac Pro, on the other hand, has removable PCIe-based graphics cards. How will Apple get the output of these cards into the Thunderbolt controller?
I’ve split this quote into two quotes for your convenience because it’s so long. Here’s quote 2:
The most likely solution is a Mini DisplayPort passthrough cable. ASUS is using an external DisplayPort cable to add Thunderbolt to its latest motherboard designs, but that seems decidedly “un-Apple-like.” There may be a more elegant solution in the works, such as directing the card’s output over the PCIe bus directly to the Thunderbolt controller, but according to our sources, no current graphics cards work that way. Given that reality, we think Apple will use an internal cable combined with GPUs featuring an internal mini-DP connector.
That’s possible, but also inelegant.
Apple doesn’t care about enabling third-party video cards, so they can do something custom here. My theory: Thunderbolt will be sent through ports on the video card’s backplate by putting a Thunderbolt controller on each video card available for this Mac Pro.