Everybody Loves Raymond took the best comedy Emmy, while instant hit Lost collected the best drama award at the ceremony in Los Angeles on Sunday.
Everybody Loves Raymond has ended after nine years
Desperate Housewives star Felicity Huffman won best comedy actress, beating two of her co-stars.
Patricia Arquette collected best drama actress for psychic crime drama Medium, while James Spader won best actor for Boston Legal for a second year.
Victims of Hurricane Katrina were remembered during the event.
Host Ellen De Generes paid tribute to them, while guests were invited to wear a magnolia, the state flower of Louisiana and Mississippi.
The awards were thinly spread around, with no show running away with a massive haul.
Everybody Loves Raymond and The Life and Death of Peter Sellers each won three awards, while Lost and Desperate Housewives collected two apiece.
As well as best drama, Lost creator JJ Abrams won for best director.
The best comedy actor award went to Tony Shalhoub for Monk, beating Everybody Loves Raymond's Ray Romano.
But Everybody Loves Raymond, which ended this year after nine seasons, did see success for Doris Roberts and Brad Garrett who won best supporting actors in a comedy honours.
Roberts, collecting her fourth Emmy, said: "This is the icing on the cake. "Nine wonderful years on Everybody Loves Raymond and to finish it off with this is wonderful."
William Shatner once again won best supporting actor in a drama for Boston Legal, while Blythe Danner, the mother of Gwyneth Paltrow, won best supporting actress for Huff.
The Life and Death of Peter Sellers, which was co-produced by HBO and the BBC, won lead actor Geoffrey Rush a best actor in miniseries or TV movie.
It also won directing and writing awards.
Dominic Monaghan (L) and Jorge Garcia star in Lost
BBC production The Lost Prince won best miniseries while Warm Springs was voted best TV movie.
Desperate Housewives had been favourite to take the best comedy award, having received critical acclaim for its first series.
It had been nominated in 15 categories but had to settle for just two, including best comedy direction.
But Daily Express TV critic Simon Edge said the fact that a single programme failed to sweep the board was good news for the TV industry.
"I imagine there must be a certain level of Desperate Housewives fatigue in the US, but it means there is room for other exciting things to come through," he said.
"I think it can be rather boring if the same programme year after year keeps gobbling up all the awards, so it is nice to have some variety."
Collecting her best actress award, Huffman thanked "the women of Wisteria Lane", her co-stars and fellow nominees Marcia Cross and Teri Hatcher - and Eva Longoria.
British actor Hugh Laurie had been favourite to win best drama actor for House, but lost out to Boston Legal's James Spader.
Collecting his award, Spader said: "I'd like to thank the academy and I'd like to thank my mother and I'd like to thank my mother again, because I forgot to thank her last year."
Sitcom Will and Grace had been nominated for 15 awards but came away empty-handed.
Mr Edge added: "These things all have their era. There was a time when Friends, then Sex and the City won everything, and the last few years they (Will and Grace) mopped up everything.
"But Will and Grace is still out there and we know where to find it. It should not consider itself snubbed."