The dark tale, which saw the serial killer claim four victims in the village, triumphed in the survey of our 12 million monthly users.
Silas, played by Jeff Rawle, murdered India Longford (Beth Kingston), Rebecca Massey (Daisy Turner), Rae Wilson (Alice Barlow) and his own daughter Heidi Costello (Kim Tiddy) during his reign of terror.
The evil grandfather also spent months tormenting nurse Lynsey Nolan (Karen Hassan), who was the only person to suspect him.
Fans finally saw Silas get his comeuppance last month, when the police realised that he was responsible for the village's sinister crimes.
Hollyoaks' series producer Emma Smithwick said today: "Thank you to all the readers on Digital Spy for voting and continuing to support the show, it's a fantastic end to a brilliant year at Hollyoaks. Long may it continue into 2012 when we have a few surprises up our sleeve for you."
EastEnders took second place in the 'Storyline' category for Max and Tanya's turbulent journey to their recent reunion, while Emmerdale was third for Jackson's assisted suicide.
Coronation Street finished fourth for Frank's evil attack on Carla, while Doctors was fifth with Lauren's murder.
> See the full list of winners from our Digital Spy 2011 reader poll Get the Inside Soap magazine on your iPhone or iPad