Chocolate

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

Chocolate was one of the many types of jelly baby owned by the Doctor. (GAME: City of the Daleks)

Uses of chocolate
The First Doctor unwittingly proposed marriage to the Aztec wise woman, Cameca, when he shared a cup of cocoa with her. (TV: 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. (TV: "Escape to Danger")

Jo Grant gave George Patrick Barnham a box of chocolates as a present after he was subjected to the Keller Machine. (TV: The Mind of Evil)

Cross confiscated a bar of chocolate from Patel. (TV: Frontier in Space)

RSM John Benton ate a chocolate bar while waiting for news of the Zygon spacecraft. (TV: Terror of the Zygons)

The Fourth Doctor gave Romana II the last Rolo in the universe. (PROSE: 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. (AUDIO: The Condemned)

A piece of Cadbury Dairy Milk chocolate, along with some chicken, formed part of the sandwich the Ninth Doctor ate to stabilise his body chemistry and neutralise the toxins of the chemical mix used against him by Charlotte Cobb, who had initially thought the Time Lord was a hostile alien like the Lend-a-Hand girls. (COMIC: The Love Invasion)

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. (TV: Planet of the Dead)

Myfanwy liked dark chocolate. It was one of the only things Myfanwy would eat without Torchwood's special "barbecue sauce." (TV: Fragments)

While hiding in the Doctor's TARDIS, Klov Dreb Fotch Passameer Day Slitheen III stole, among other food, chocolate biscuits. (COMIC: Who Ate All the Biscuits?)

Other references
Jamie McCrimmon and Driver Evans came across a platform vending machine selling bars of Camfield's Fairy Milk Chocolate at St. Paul's tube station. Fancying some chocolate, Evans tried the machine without inserting any money and discovered, to his surprise, there was a bar in the machine's open compartment. (TV: The Web of Fear)

On a planet visited by the Second Doctor and Jamie, King Conrad ordered his Scientist Royal to invent calorie-free chocolate. (PROSE: Twin Piques)

On Colony 34, outside the walls of third city, chocolate was one of the many items that was very hard to obtain. (AUDIO: 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 Sixth 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. (AUDIO: The Marian Conspiracy)

The Tenth Doctor and Martha Jones travelled the universe in search of the perfect chocolate milkshake. (COMIC: Agent Provocateur)

Anji Kapoor was a lover of chocolate. Once, when she, Trix, Fitz and the Eighth 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. (PROSE: Timeless)

Clara Oswald liked chocolate. (TV: Last Christmas)

Behind the scenes
The Twelfth Doctor's letter in DWA15 12 mentions Juevos VI, a moon made of chocolate. According to the Doctor there wasn't much to do on Juevos VI because eating the chocolate was illegal.

Doctor Who chocolates

 * 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
 * Doctor Who-themed 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.