The leading nominee was the gritty, unsparing World War II drama, The Pacific, with 24 nominations.
Conan O'Brien is gone from The Tonight Show but his short tenure as host is not forgotten: The late-night show with him at the helm nabbed a nomination as best variety, music or comedy series, while resurrected Jay Leno was snubbed in the category.
David Letterman's Late Show also was missing from the nominees, after a season in which the host turned an admission of affairs with female staffers and a blackmail attempt into high broadcast drama.
Besides Glee, other newcomers receiving Emmy recognition include Modern Family, with nods for best comedy series and for five members of its ensemble cast - although not linchpin Ed O'Neill as the patriarch - and The Good Wife, a nominee for best drama and recognition for star Julianna Margulies.
The final season of Lost garnered nominations for best drama series and a nod for star Matthew Fox and supporting nominations for Terry O'Quinn and Michael Emerson. Elizabeth Mitchell received a guest actress bid for the drama.
Saturday Night Live received 12 nominations for a total 126 nominations during its run, surpassing the ER all-time record of 124 bids. One of the nominations went to Betty White, who at 88 proved you're never too old for comedy when she hosted the show to big ratings and applause.
White's competitors include Tina Fey, the former Saturday Night Live writer and star who took a break from her 30 Rock, the second-most nominated comedy with 15 bids, to return as an SNL host.
Fey made light Thursday of her best comedy actress nomination for 30 Rock.
"This is great and exciting news. Also, this seems like an appropriate time for me to announce to NBC that I will not be renewing my contract - with my gym," Fey said in a statement. Of the show's best comedy series bid, she added, "We're grateful and excited. Especially since today is the fifth anniversary of the day NBC forgot to cancel us."
Mad Men was the most-nominated drama with 17 bids. The darkly sexy 1960s period show has been honored as best drama two years in a row. Its stars, Jon Hamm and January Jones, received acting bids.
Besides Glee and Modern Family, other nominees for best comedy series include Curb Your Enthusiasm, Nurse Jackie, The Office and last year's winner, 30 Rock. The comedy has won three times in a row.
Joining Mad Men, Lost and The Good Wife as best drama series nominees were Breaking Bad, Dexter and first-timer True Blood, which overcame TV academy voter reservations about fantasy genre shows.