Both the Establishing Shot of Baker Street in the first episode and the layout of Sherlock's flat are essentially a modern day versions of their counterparts in the Jeremy Brett series. In the case of the apartment it's right down to the arrangement of the furniture.
In the pilot, while Sherlock checks his e-mail, he responds in regards to a church bell theft that "Davies is your man".
In "A Scandal in Belgravia," the 1,895 hits that John's blog gets stuck on is a Shout Out to Vincent Starrett's poem "221B," which ends with the words "and it is always eighteen ninety-five". Particularly appropriate to a TV series that's reimagined the characters in modern times, given that the poem is about how Holmes and Watson are timeless.
At one point in "A Scandal in Belgravia", John Sherlock and Irene are in 221B, and Sherlock says that he put her phone into a safe-deposit box. John's suggestion that "Molly can get it, and then have one of your homeless network members bring it here" is reminiscent of the final act of The Maltese Falcon, when Sam Spade leaves the titular artifact in a safe-deposit box, mails the ticket to another box, and then calls his secretary to get first one then the other, and bring it to his office, where he and the other principal characters are waiting. And then Sherlock immediately subverts the whole situation by pulling the phone out of his pocket.
Watson's remark about fighting the urge to steal an ashtray at Buckingham Palace is very likely to be a reference to an incident in which British TV host Denise Van Outen stole not just an ashtray, but also a tissue box (although she did return them both). The fact that the ashtray was made of glass is likely also a reference to the Michael Fagan incident, as he broke a glass ashtray and cut his hand when he "visited" Buckingham Palace for the second time.
Mycroft's three-piece suit and ever-present malacca-handled umbrella could be a nod to John Steed. Mycroft often strikes a similar pose to Steed's, leaning on the umbrella with one hand, and with one leg crossed behind the other.
At the beginning of "The Reichenbach Fall," John's statement that "My best friend, Sherlock Holmes, is dead" sounds very familiar to Rose Tyler's This is the story of how I died.
Speaking of films and Moriarty, what is the climax of the plot in "The Empty Hearse?" The same as in V for Vendetta, a hidden subway station hides a car rigged with tons of explosives, which will travel along the track to Parliament and blow the building up. Just to drive the parallel further, it takes place on Guy Fawkes Night, the 5th of November.Sound familiar?
During "The Hounds of Baskerville", Sherlock (while under the effect of a fear-inducing drug) explains his usual disregards to sentiments. John calls him Spock as a response. Bonus points for the nickname coming a few lines after Sherlock reminds us of his famous phrase, "when you have eliminated the impossible", a line also used by Spock during Star Trek VI: The Undiscovered Country. It's a Mobius strip shout-out !
Another Star Trek reference is when Captain John Watson, at Sherlock's 'grave' in The Reichenbach Fall, makes a speech calling him the "Most human human being that [he's] ever known." This bears a striking resemblance to Captain Jim Kirk's speech at Spock's funeral at the end of Wrath of Khan, saying that "of all the souls [he] have encountered in all of [his] travels, [Spock's] was the most human.
Also in "Hounds", Sherlock analyzes words like John Anderton analyzed dreams in Minority Report.
In "A Study In Pink" Sherlock and John walk past a hair salon on Charlotte Street en route to a cafe where they plan to stake out the killer. This places the cafe on Rathbone Street, which they must then run down in a chase scene. Basil Rathbone played Sherlock Holmes in over a dozen films.
Also in "A Study In Pink", Sherlock hops up onto his chair in a way very reminiscent of Jeremy Brett (who does it in 'The Adventure Of The Empty House', among others).
One of newspapers on screen after Moriarty's trial in "The Reichenbach Fall" has a line in it that read 'In a twist worthy of Conan Doyle.' Arthur Conan Doyle is of course, the creator of Sherlock Holmes.
When in hiding in the lab during the events of "The Reichenbach Fall," Sherlock bounces a ball off of the cabinets across from him the same way that Steve McQueen does in The Great Escape.
The season 3 opener The Empty Hearse, Sherlock texts Mycroft about LAZARUS. Mark Gatiss played Dr. Lazarus in the Doctor Who episode "The Lazarus Experiment".
On the "Hollow Client" entry of John's blog, Sherlock formulates many theories as to how the the titular client could turn himself invisible: one theory is that he was "dressed up in the same fabric as the chair". A similar technique another world famous detective employed in A Game of Shadows. And it's one big shout out to The Invisible Man.
In "The Sign of Three" one of the flashbacks to previous cases has Sherlock holding a matchbox, the only one of hundreds that wasn't empty, and when asked what was in it he says that it's "inexplicable" as he opens it and a golden light shines on his smiling face much like the briefcase in Pulp Fiction.
In "The Sign of Three" Sherlock's drunken analysis of items in the flat includes a reference to the animal skull as "deaded", a term largely associated with The Goon Show.
In "His Last Vow" Mycroft calls Sherlock a “a scalpel wielded with precision” in comparison to a "blunt instrument". A "blunt instrument" was Ian Fleming's traditional description of James Bond. It's also often used to distinguish their characters: Sherlock takes down criminals by analysing and figuring out their methods, while the books' James takes down criminals using force.
Befitting of a professional assassin, Mary Watson wields a suppressed Walther PPK, Bond's signature weapon, to threaten Magnussen, shoot Sherlock and show off her terrifyingly good aiming skills.
In "Scandal in Belgravia", the flight number associated with Mycroft's plan to foil a terrorist plot to blow up a Jumbo Jet, said jet's flight number is "007". Naturally, and quite unsubtly, the operation is referred to as "Bond Air".
The Great Game's Golem is very similar to a bald Jaws, down to maintaining a teeth-flashing smile throughout his fight with Sherlock for no apparent reason. This only makes sense as Jaws is also described as the best and most expensive assassin-for-hire in the business (aside from Scaramanga).
During the Book search in "The Blind Banker", Freakonomics and Transition are featured prominently.
In "The Abominable Bride", the outfits of the secret society closely resemble the outfits of the conspirators from a certain Tintin adventure. Resemblance to the KKK is an unfortunate side-effect. Then again, all three such organizations are not exactly standing on the moral high ground.
In "The Blind Banker", Sherlock's line about "You want to hide a tree in a forest" is a paraphrase of Father Brown in "The Sign of the Broken Sword" ... and a much closer paraphrase of the Doctor quoting Borusa paraphrasing Father Brown in "The Invasion of Time".