It's already being reported.
From USA Today:
Recovering quickly from an ill-timed plane crash joke that opened his introductory clip package, O'Brien bounced through an amusing salute to the TV year â€” from a stop on the Lost island to a reprise of South Park's Tom-Cruise-in-the-closet joke. By the end, he had built up so much goodwill, you were willing to cut him some slack over his clumsy musical spoof of NBC's ratings â€” a bit that was far too NBC-centric for an evening that is supposed to belong to the entire industry.
From The Detroit News
From there O'Brien went on to "The Office" then "24," Fox's "House," ending the sketch inside an episode of the animated Comedy Central hit "South Park" with an obvious but funny Tom Cruise out of the closet joke.
This is only a few hours after the show. There are more articles out there that mention it already - including ones in the NY Times and Variety - but I can't see them without subscribing. ;p
Even if South Park had won the Emmy it would not have appeared on the show. The people making the show gave Trapped in the Closet
MORE exposure than an Emmy win would get by making it part of the opening segment.
What appeared to Davey to be a "win" got turned and shoved down his throat. Can't wait until the video is available. The enthusiastic cheering from the live audience when the animated Conan went into the closet with Tom was priceless...