EastEnders' other wins included the best actor prize for Robert Kazinsky, the best comedy performance gong to Nina Wadia, and the award for dramatic performance from a young actor to Maisie Smith.
On the red carpet outside the ceremony at BBC Television Centre, west London, actor Steve McFadden said: "It's the best soap: it's well written, well acted, the camera team are fantastic.
"We've got high production values. I won't say, 'No expense spared,' but you don't move on until you've nailed the scene and that's really important."
EastEnders won the top prize, beating Coronation Street, Doctors, Emmerdale and Hollyoaks, for the second year running.
Windsor, who has been in the show since 1994, said: "We all know what we go through; we're doing about eight episodes at the same time, all across each other, and they are long hours."
But she added: "I love it, I love the whole process of this."
Coronation Street's Katherine Kelly was named best actress, with the show's Craig Gazey recognised with the best newcomer prize.
The successes for Doctors included the best storyline accolade, for Vivien March's rape, with the actress who played her, Anita Carey, winning the dramatic performance prize.
Coronation Street writer Peter Whalley collected an achievement award.
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