The Emmys are standing with Team Coco, snubbing Jay Leno.
O'Brien's short-lived reign at NBC's "Tonight" show earned him an Emmy nod for best variety, music or comedy series. Leno, who returned to "Tonight" following the failure of his prime-time show, was not nominated on Thursday.
But if it makes Leno feel any better, David Letterman was snubbed in the same category — for the first time in 17 years.
NBC submitted both versions of "Tonight" for Emmys consideration, letting the TV academy decide what to include in the category. They went with O'Brien, who was nominated alongside "Saturday Night Live" and shows hosted by Jon Stewart, Stephen Colbert and Bill Maher. O'Brien's final "Tonight" show was also nominated for best writing in a variety, music or comedy series.
"Congrats to my staff on 4 Emmy nominations," O'Brien said in a message posted on Twitter. "This bodes well for the future of the `Tonight' show with Conan O'Brien."
It may bode well for his future: O'Brien gets back to television with a TBS late-night show this fall, and he has some critical wind at his back.
"Everybody understands what happened," said Don Mischer, executive producer of the Emmy Awards telecast, scheduled to air on NBC next month. "And it was an opportunity for Emmy voters to like give him some support, you know. And he deserved it."
NBC issued a statement congratulating O'Brien "and all of our nominees."
Anyone who questions whether the TV academy is letting moral judgments influence creative ones would have ammunition for their arguments in Letterman and Charlie Sheen.
Letterman's "Late Show" on CBS has been nominated every year since it began in 1993. Not this time, when his eligibility period coincided with a well-publicized extortion attempt and Letterman's admission that he had relationships with some of his staff members.
Charlie Sheen, star of television's most popular comedy, "Two and a Half Men," was not among the six nominees for best actor in a comedy after he had received nominations in the category for the previous four years. Sheen has been involved in his own messy, personal incident, an alleged domestic violence case against his wife on Christmas Day. The CBS show was not among the nominees for best comedy.
After being an Emmy darling last year for scoring the first best comedy nomination for an animated series in nearly 50 years, Fox's "Family Guy" this year was only nominated for music included in one episode.
One Emmy snub may make for delicate moments on the set of ABC's freshman comedy "Modern Family." Five members of the show's ensemble — Julie Bowen, Sofia Vergara, Ty Burrell, Eric Stonestreet and Jesse Tyler Ferguson — earned supporting actor or actress nominations. The sixth member, and perhaps the best-known actor in the cast, Ed O'Neill, was not nominated.
Burrell, who plays O'Neill's son-in-law, said O'Neill "is the heart and soul of our show.
"But in an interesting way, I think this may actually bring some attention to the fact that he really is the core of our cast," Burrell said of the snub. "So I'm simultaneously starting a campaign for Ed O'Neill for either write-in or next year."
Fully half of the supporting actor nominees for a comedy are on "Modern Family." Stonestreet and Ferguson play the gay couple on the show.
"We're a family," Stonestreet said. "Jesse was the first person I called. I just told him this is amazing because this is a validation that people have embraced and accepted and believed the couples on our show."
NBC's critically acclaimed but audience-starved drama "Friday Night Lights" broke through this year, with Kyle Chandler and Connie Britton both getting nominations for best actor and actress. Both were considered surprises.
For all the attention paid to O'Brien, Leno and Letterman in late-night, HBO's Bill Maher has a chance to extend a dubious streak. He received four nominations Thursday for his talk show and an HBO special, giving him a career total of 26.
He has never won.
Associated Press Television Writer Lynn Elber and Entertainment Writer Sandy Cohen in Los Angeles, and Entertainment Writer Jake Coyle in New York contributed to this report.
(This version CORRECTS Corrects penultimate paragraph to note that Bill Maher has 26 career Emmy nominations, not 24, and not all are for his `Real Time' show.)
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