Whoa. Thunderbolt must be extremely upset about having to share the spotlight with USB 3.0 on the new Mac models introduced yesterday, as Thunderbolt Software Update 1.2 (also released yesterday) is now causing boot failures.
The issue was reported by TidBITS publisher Adam Engst this morning, who said that people are reporting "strange boot-related problems" such as kernel panics, lockups at the gray boot screen, "unexpected error" messages and other issues. It's a pretty serious problem -- the Macs are unusable after the update.
Adam reports that the best fix at this point is to reinstall Lion. That's quite easy with Lion, although time consuming. Users need to boot into Recovery Mode during restart by holding down Command-R. Once booted, they can select "Reinstall Mac OS X". If you don't have a Recovery HD volume, then Lion Internet Recovery will take over and allow you to download a new Recovery HD image to boot from.
Once Lion is reinstalled, do not reinstall Thunderbolt Software Update 1.2 unless you're a masochist and like to reinstall operating systems. If you have a Thunderbolt-equipped Mac and have not run the update yet, avoid it like the plague. It's only required for the new Thunderbolt to Gigabit Ethernet Adapter anyway.