Danes, who captured her second trophy for the terrorism drama, paid tribute to one of the series' writers, Henry Bromell, who died in March and who received a writing Emmy posthumously Sunday.
"Breaking Bad," the brutal drug-fueled saga of an everyman's ambition turned evil, captured its first best drama Emmy.
The ceremony often struck a melancholy note with extended tributes to stars and other industry members who died in the past year. Danes' win ended the hopes that "Scandal" best actress nominee Kerry Washington would become the first African-American to win in the category since Cicely Tyson in 1995 for "Sweet Justice."
Julia Louis-Dreyfus claimed her second consecutive best comedy actress award for her role as an ambitious political second banana in "Veep," with Jim Parsons again claiming the top comedy acting trophy for "The Big Bang Theory."
"I'm very grateful to have the opportunity to make people laugh. It's a joyful way to make a living," said Louis-Dreyfus.
Parsons added to the awards he won in 2011 and 2010 for the role of a science nerd. "I want you to know I'm very aware of how exceedingly fortunate I am," he said.
Merritt Wever of "Nurse Jackie" won the night's first award, for best supporting actress in a comedy series, kicking off the ceremony.
Tony Hale of "Veep" claimed the trophy for best supporting actor in a comedy, a category that has been the property in recent years of the men of "Modern Family."
Laura Linney was named best actress in a miniseries or movie for "The Big C: Hereafter." "The Voice" won best reality-competition program, and Tina Fey won for writing "30 Rock."
Michael Douglas was honored as best actor for his portrayal of Liberace in "Behind the Candelabra," besting his co-star Matt Damon. The film also captured a top trophy as best movie or miniseries.
Bobby Cannavale, from "Boardwalk Empire," won as best supporting actor in a drama. Anna Gunn from "Breaking Bad" won the best actress award in the same category.
Derek Hough of "Dancing with the Stars" won the trophy for best choreography.
In the variety show category, "The Colbert Report" broke a 10-year winning streak held by "The Daily Show with Jon Stewart." It also won for best writing for a variety show.
Among those honored was Cory Monteith, the "Glee" star who died at age 31 in July of a drug and alcohol overdose. "His death is a tragic reminder of the rapacious, senseless destruction that is brought on by addiction," said his co-star Jane Lynch.
The inclusion of Monteith despite his abbreviated career and the exclusion of such enduring stars as Jack Klugman and Larry Hagman drew criticism from some. Adam Klugman, son of "The Odd Couple" actor, called his father's omission "criminal."
Edie Falco recalled her late "The Sopranos" co-star James Gandolfini, saluting him for his "fierce loyalty" to his friends and family and his work with military veterans.
"You all knew Jim the actor. I was lucky enough to know Jim the man," she said.