The Channel 5 reality show received over 2,000 viewer complaints - 12.5% of the 16,000 issues registered with the regulator.
Most Big Brother complaints related to contestant Conor McIntyre's apparent bullying of Deana Uppal.
In November, Ofcom ruled that the series breached its broadcasting code by airing the footage. Channel 5 was also accused of misleading viewers over Facebook voting.
The X Factor Results Show and Phillip Schofield's alleged paedophile list stunt on This Morning came second and third respectively.
Many X Factor complaints surrounded accusations that the results had been fixed when Carolynne Poole was eliminated ahead of Rylan Clark.
The subject of most This Morning complaints related to Schofield handing the Prime Minister a list of alleged paedophiles live on TV.
ITV later had to pay Lord McAlpine £125,000 in damages after his name was involved in the stunt. Schofield was also disciplined by ITV.
Most complained-about shows of 2012 (as of December 12):
1. Big Brother (Channel 5) - 2,088
2. The X Factor Results Show (ITV1) - 1,488
3. This Morning (ITV1) - 811
4. True Stories: Gypsy Blood (Channel 4) - 509
5. Live: The Silent Ascent (Sikh Channel) - 378
6. Sky News - 364
7. Islam: The Untold Story (Channel 4) - 293
8. The X Factor (ITV1) - 305
9. Citizen Khan (BBC One) - 256
10. Keith Lemon's LemonAid (ITV1) - 246