The show netted four awards, for best supporting actress and actor, as well as best direction and best writing.
"Glee" star Jane Lynch hosted the 63rd annual award show in Los Angeles, singing, dancing and gently poking fun at the industry.
Other big winners included Manhattan's "The Daily Show," which won best comedy and best variety series for the 9th straight year, beating sister show "The Colbert Report".
New York City-based "Mad Men" won best drama for the fourth consecutive year.
And even "winning" actor Charlie Sheen made a cameo appearance, handing out the award for best comedy actor.
“I want to take a moment to get something off my chest, to say a few words to everyone here from 'Two and a Half Men.' From the bottom of my heart, I wish you nothing but the best for this upcoming season," he said in a rare moment of humility.
Legendary New York director Martin Scorsese also won his first Emmy for his directing work on "Boardwalk Empire".
"I've always dreamed of working on a project where the characters can develop over a period of time," Scorsese reportedly said backstage. "You can develop plot, characters ... and get more done over a longer period of time. It gives you more license and much more freedom."