When offered a cup of tea, Sherlock replies that he'd need something stronger - 7% stronger. The original Sherlock Holmes used a 7% solution of cocaine when he didn't have a case and "wanted to stimulate his mind."
Sherlock knows that Lestrade just returned from holiday because of his tan. In real life, Rupert Graves was tan because he had just returned from Guadeloupe while filming Death in Paradise (2011). His tan was written into the script.
The quote "Once you've ruled out the impossible, whatever remains, however improbable, must be true" (from Sir Arthur Conan Doyle's 'The Sign of the Four') is used by Sherlock. A minute later Watson jokingly calls him "Spock." In Star Trek VI: The Undiscovered Country (1991), Spock uses the same line, stating that an ancestor of his used the same quote.
Watson's reference to Holmes as "Spock" is interesting as a number of plot lines in the various incarnations of Star Trek have circled around Sherlock Holmes, including both Spock and Data uttering Holmes' most famous quote: "when you have eliminated the impossible, whatever remains, however improbable, must be the truth." This highlights the similarities between these Spock and Holmes, and how ingrained each is in popular culture.
Sherlock explains the bet he had with Watson about the presence of a hound to get information from the "monster" tour guide. In "The Adventure of the Blue Carbuncle", Sherlock holds a bet with a salesman to get the true source of a sold goose.
In the scene where Sherlock is looking through the information on H.O.U.N.D.S when the screen says "frontal lobe damage" Jim Moriarty's screaming face briefly shows up among the other faces that flash by.