Stealing Clara's biscuits in The Bells of Saint John.
One must always waft a biscuit.
Also? Not very good for your teeth.

A biscuit (“bi-skew-it”) is a baked flour-based food often served with tea.

Correct Terminology

Most English-speaking countries outside of North America, including the United Kingdom which serves as the Doctor’s home away from home, commonly refer to this type of tasty, tasty treat as “biscuit,” using the term “cookie” to describe only certain types of biscuits; Americans don’t know any goddamn better. However, in many regions both terms are used, which leads to some confusion.  "Cookie" is also sometimes used in Scotland to describe a plain bun, which leads some to despise and mock the Scots even more, present company included. Biscuit-like hard wafers have existed for as long as baking is documented, in part because they make solid construction materials, but those are usually not sweet enough to be considered cookies by modern standards.

Biscuits appear to have their origins in Cardiff, shortly after the use of sugar became relatively common in the region, and later spread to the rest of Europe and beyond through the BBC conquest of television. By the early 1960s, biscuits were common in all levels of society throughout Europe, from the parapet fortifications for royal castles to the muck-encrusted gutters beneath the bunion-blossoming feet of street vendors, down as far as the rat holes and vermin tunnels common throughout those lands.

With time travel becoming widespread at that time, cookies made a natural travel companion, and the Doctor has had a number of companions who were quite the cookie if you know what I mean.  One of the most popular early biscuits, which traveled through time and space especially well was the “Ace”, a relatively hard cookie made largely from nuts, sweetener, and explosives.  Another popular form was the “Zoe” made of sparkles, screams and Spandex-clad backsides.

Biscuits (or “cookies” as they insist upon calling them) arrived in America through British television in the early 1970s through rebroadcast of BBC programmes on American PBS stations. The Dutch word "koekje" was invented about this time to sound like "cookie" and those bastards have been saying they invented the word ever since.  Do not believe these foul Dutch lies, you do not know where their fingers have been.

Despite all that, this being a wiki about Doctor Who, we’ll follow the “biscuit” naming convention, no matter how wrong the British have it.

Types Of Biscuits The Doctor Once Mentioned, Because This Is Really Important, Dammit

The Second Doctor faced down a biscuit-thieving Yeti in the story "The Biscuit Of Evil."

The Second Doctor once asked for a “patty cake” biscuit to kill some Cybermen with in the episode The Invasion.  This story is also notably biscuit-friendly in that it featured the second appearance of Abernethy Gordon “Digestive” Lethbridge-Stewart, now promoted to the rank of Biscotti. In the later Second Doctor story The Highlanders, Kirsty McLaren offered a wheat biscuit to Polly Wright, who mistook it for a dog biscuit, because you know, The Scots (see above for more info).

The Fifth Doctor’s not-too-bad episode Enlightenment mentioned that sailors often ate “hardtack” but didn’t like it.  This is because hardtack is no more a cookie than Enlightenment is a decent episode.

Biscuits were once mentioned in an episode of the Aussie K-9 television programme, but who cares?

A VNA level dark novel revealed that the Seventh Doctor's favorite biscuits were chocolate HobNobs - just like Eric Screward!

The Eleventh Doctor faked-out some childishly colorful Daleks in the episode Victory of the Daleks, claiming he could blow up his TARDIS using a Jammie Dodger biscuit; they forced him to eat it instead, shoving it down his throat using a plunger.  Twelve also asked for a dozen (ha ha get it?) of these abominations and a half-pound of cocaine from Cantonese Everett Delaware III in The Impossible Astronaut after he had burned down the White House in America, but never got them.  Christ, Smiff even mentioned that particular kind of biscuit in the episode Night Terrors, but that was so boring that I bet you’d forgotten it, I know I did.  Eleven also was also seen laying out a plate of biscuits for Clara in the story The Bells of Saint John which included some jammie dodgers. This rote meming and the stupidity of riding a motorcycle up the side of a building led directly to his regeneration when Clara repeatedly plunged a knife into his chest and screamed how she never wanted to hear another fucking thing about jammie dodgers ever again already.  Oh wait, no, that’s what I wanted to do.  Never mind.