I happened to tune in Thursday during the "Branch Closing" episode and there was definitely new footage (oddly enough, I had just seen the original version on an airplane a few days earlier). I think this episode had a "producer's cut" online at the original airing, though, so it might have already existed this way. The following episode where the new employees came to Scranton was just like it originally aired.
Re-reading your question, I think you might have been addressing the wrap-around material with Steve Carell? The ones at the very end of last Thursday's marathon just had him talking about 'Evan Almighty' against a backdrop of same.
Scott, the content is all over the place so it's difficult to answer the question in a general sense. I'll recount some of what I know off the top of my head ...
On the March 15, 2007 "Newpeats", the "Travelling Salesmen" episode had some new footage that was not originally broadcast, nor had it appeared on the NBC website as deleted scenes, nor had it appeared on the iTunes version. It was a completely new story line about Pam winning an art contest.
The "Return" episode from that same night had an epilogue about Andy that was not originally broadcast, but appeared in a "Producer's Cut" that was viewable online on NBC's site for about a week. The producer's cut was also the iTunes version. The episode had a few bits and pieces cut out of the original broadcast version to make room for this new ending (and possibly because of the new footage in "Travelling Salesmen") and additionally did not feature all of the footage in the producer's cut.
On the March 29, 2007 "Human Resource Nightmares" marathon, there were newly shot wraparound scenes with Paul Lieberstein (Toby), Mindy Kaling (Kelly), and Angela Kinsey (Angela) that were quite amusing. The five episodes were the broadcast originals, as far as I know.
On the June 21, 2007 four-episode set hosted by Steve Carell ...
"Casino Night" was originally broadcast as "super-sized" (about 40 minutes with commercials) and was broadcast unchanged.
"Branch Closing" was the "Producer's Cut" that had been available on-line at NBC.com and on iTunes, but was not originally broadcast at that length. Most of the new scenes featured Creed and Meredith, but there were other bits and pieces as well.
"The Merger" was originally broadcast super-sized, but had some footage cut out to accommodate the "Evan Almighty" hosting footage.
I didn't see all of the Carell marathon, so I don't know if he shot any Office-centric footage. Everything I saw was about "Evan Almighty".
I don't know what the episodes scheduled for the June 28, 2007 "marathon" will be like.