Chocolate

Chocolate was a food made from cocoa, enjoyed by humans. Because it was naturally bitter, it was often sweetened with sugar.

References

The First Doctor unwittingly proposed marriage to the Aztec wise woman, Cameca, when he shared a cup of cocoa with her. (DW: The Aztecs) In a later adventure, the First Doctor offered Vicki some chocolate to assuage her fears that Ian might be in danger. She, however, refused the gift. (DW: "Escape to Danger")
The Fourth Doctor gave Romana the last Rolo in the Universe. (ST: Do You Love Anyone Enough?)
The Sixth Doctor once survived being poisoned with aspirin by eating chocolate, which contained simple triglycerides that counteracted the aspirin's effect on Time Lord physiology. (BFA: The Condemned)
On Colony 34, outside the walls of third city, chocolate was one of the many items that was very hard to obtain. (BFA: LIVE 34)
Evelyn Smythe loved chocolate so much that even on her initial trip in the TARDIS, she insisted upon bringing her own supply of hot cocoa mix. Indeed, she was a master baker of chocolate cake, and the Doctor had to use the promise of picking up some specialty chocolate in Mexico or Havana just to get her to travel in the TARDIS at all. (BFA: The Marian Conspiracy)

Leela eats chocolate for the first time (DW: The Face of Evil)

The Tenth Doctor and Martha Jones travelled the universe in search of the perfect chocolate milkshake. (IDW: Agent Provocateur)
The Tenth Doctor enjoyed a chocolate Easter egg, but then passed it to Lady Christina de Souza after becoming concerned that its sugar content might harm his teeth. (DW: Planet of the Dead)
Myfanwy liked dark chocolate. It was one of the only things Myfanwy would eat without Torchwood's special "barbecue sauce." (TW: Fragments)
While hiding in The Doctor's TARDIS, Klov Dreb Fotch Passameer Day Slitheen III stole, among other food, chocolate biscuits. (WC: Who Ate All the Biscuits?)
Anji Kapoor was a lover of chocolate. Once, when she, Trix, Fitz and the Doctor were travelling between parallel versions of the Earth, they encountered an Earth where chocolate had never been invented. They quickly moved on from that Earth. (EDA: Timeless)

Karen Gillan is particularly fond of organic chocolate. (CON: "Charlie McDonnell - Christmas Presents (badger)")
Coincident with season 8, Nestlé issued the Nestlé's Doctor Who milk chocolate. It came in 15 collectable wrappers, each of which had a tiny instalment of a story called Doctor Who Fights Masterplan "Q", starring the third Doctor, Jo Grant and The Master
Doctor Who-themed Advent calendars have been issued on several occasions; a recent version was the Bon Bon Buddies 2010 Doctor Who Milk Chocolate Countdown Calendar based upon series 5 Daleks.