Dr Who's teary goodbye to assistant and love interest Rose beat classics Star Wars and Alien to the top spot.
The identity of the Doctor to replace Matt Smith will be announced on television tonight with Peter Capaldi still the bookmakers' favourite
Betting on the next Dr Who has been suspended by a bookmaker after unconfirmed reports that Rory Kinnear has been offered the role.
Dr Who has been named best drama at the National Television Awards.
Receiving the award, Jenna Coleman said: "50 years and still going strong - well done Who!"
Watch the National Television Awards live on ITV and you can catch up later on ITV Player.
Matt Smith has been honoured for 'best drama performance' at this year's National Television Awards for his role in Dr Who.
The Countess of Wessex met Matt Smith, Tom Baker, Peter Davison, John Hurt and a pair of Daleks at a reception at Buckingham Palace to mark the 50th anniversary of Doctor Who.
There were also two versions of the Tardis and K-9 the robot dog set up in the Palace's Bow Room.
The Daleks will be among the foes to return for the 50th anniversary special of Doctor Who.
The creatures celebrate their own half century this year and will appear in the BBC1 show to mark the milestone in a show which will unite Matt Smith with his predecessor in the role of the Doctor, David Tennant.
The episode will also see the return of Billie Piper - who played Rose Tyler - as well as Jenna Coleman, who has been seen by viewers during the most recent series as Clara Oswald.
When the Daleks make their return they will be in their original design, the classic look had been updates in 2010.
The programme's lead writer and executive producer Steven Moffat said: "The Doctor once said that you can judge a man by the quality of his enemies, so it's fitting that for this very special episode, he should be facing the greatest enemies of all."
The man who first brought Doctor Who to British screens has criticised the current series for being too sexy.
Waris Hussein, who directed the first episodes of the long-running science fiction show when it began in 1963, said he has been unimpressed by Jenna-Louise Coleman's character's romantic relationship with Matt Smith's version of the Time Lord.
"There is an element now, and I know we're living in a different era, of sexuality that has crept in," he told BBC Radio 4's The Reunion.
"The intriguing thing about the original person was that you never quite knew about him and there was a mystery and an unavailability about him," he added. "Now we've just had a recent rebirth and another girl has joined us, a companion, she actually snogged him."