UPDATE 2: Macworld has confirmation from Apple that the new iMacs will support Target Display Mode but only when the device they are connected to is also a Thunderbolt-equipped Mac; the trick won't work with older mini DisplayPort models.
So a new MacBook Pro connected to a new iMac will work, but older MacBook Pros will not, and a current MacBook Air won't work either. This also means the popular Kanex adaptors (which convert HDMI signals to mini DisplayPort ones, letting users plug things like games consoles into their iMacs) probably won't work with the new iMacs -- we've contacted Kanex to ask for confirmation.
This change is probably tied to the mini DisplayPort being replaced by two Thunderbolt ports. Whatever clever hack Apple did to make the mini DisplayPort connection bi-directional in the earlier iMacs is presumably difficult or impossible to replicate through Thunderbolt, as they have less control over the protocol (remember that Thunderbolt is an Intel design, and uses a special Intel communications chip).
UPDATE 3: Consider that, for legacy mini-DisplayPort devices to work, the Thunderbolt interface would need to consume a raw display signal -- not one wrapped up in the clever Thunderbolt protocol (note, PDF link) which combines PCIe and DisplayPort data into a single stream. This is probably why the new Thunderbolt ports cannot maintain backwards compatibility with older devices. However, when the device sending the signal also has Thunderbolt, they can negotiate a way to send the signal that the receiver can understand.