- Word of God confirms that Angus the phrenology bust is a prop from House, another show that took a twist on the Sherlock Holmes mythos.
- The Running Gag of Holmes introducing Watson in amusing ways may be a Shout-Out to the comedic version of Holmes seen in Psych which is more like Holmes than the premise might seem.
- The phrase "I believe in Sherlock Holmes" seems to be one to their Transatlantic Equivalent show.
- The Rube Goldberg Machine in the Title Sequence is a live-action version of Ratigan's trap from The Great Mouse Detective.
- Marcus Bell is the only main character without a counterpoint from Doyle's original stories. But Dr. Joseph Bell was a mentor for Arthur Conan Doyle and an inspiration for Sherlock Holmes.
- In "One Way to Get Off", the perp's name is Crewes, and we spend a good deal of the episode thinking he spent 13 years in prison wrongfully because of planted evidence. Sound familiar, Life fans?
- "The Leviathan":
- Holmes is hired by Casterly Rock Security to solve a robbery of one of their bank vaults.
- Joan Watson's brother's name is Oren, a nod to Lucy Liu's character in Kill Bill. Doubles as Actor Allusion.
- Holmes loudly plays Ludwig van Beethoven's Ninth Symphony ("Ode to Joy") when he figures out the perpetrators of the vault heist. This is the same music played when the criminals succeed in Die Hard, which also featured a multiple-level "impenetrable" vault.
- In "The Red Team" Holmes has to find the identities of the people who participated in a classified government operation, one of which is a mathematician named Harold Dresden. One of the suspects has the code name of "Yossarian".
- The episode is also about a war game that simulates military scenarios, and it involves a red team and a blue teamnote .
- In the first season finale, "Heroine":
- "Solve For X" revolves around an equation that can be used to crack any known type of digital security, much like Moriarty's "skeleton key" in "The Reichenbach Fall". Unlike Sherlock's version, this one is not only real, but it already exists, though it still has to be custom-programmed for specific targets.
- "All In The Family" is an hour-long string of references to The Godfather. And of course, the episode title is a reference in its own right.
- The conversation in "Dead Clade Walking" reverse the conversation between Watson and Irene from Sherlock's "A Scandal in Belgravia":Gay: I'm Gay.
Holmes: I'm not.
- The fighting cocks from "The One Percent Solution" are named Romulus and Remus, after the two brothers who founded Rome in Classical Mythology. In the myth, Romulus kills Remus, but by the end of the episode Sherlock teaches his cocks to get along.
- Mycroft, a British spy produces a Walther PPK when startled in bed with a lover.
- Sherlock notes that a Gentleman Thief is nicknamed "Raffles" after the protagonist of a series of novels written in Victorian Britain by E. W. Hornung. Also a Mythology Gag because Hornung was Arthur Conan Doyle's brother-in-law and Raffles was intended as the original Holmes' Evil Counterpart.
- Joan says "That escalated quickly."
- While discussing the possibility of an AI committing a murder Mason quotes Kyle Rees' speech about how the machines won't stop from The Terminator, something Joan quickly lampshades.Sherlock: Mason, unless the machines rise tonight, we have a murder to solve.
- In "Dirty Laundry", Holmes says that a spy "might as well have a phone in your shoe"... an apparent reference to Get Smart and its infamous Shoe Phone.
- Holmes makes another Get Smart reference in "Rip Off"; concerned that Joan's memoirs might reveal his secrets, he tells Kitty that "I find it necessary to circumscribe a razor-sharp cone of silence."
- In "A Regular Irregular", Harlan Emple names two other puzzlehunts, the real Cicada 3301 and the apparently fictional Octarine's Challenge.
- "T-Bone and the Iceman" contains a Shout Out that's so unexpected, it's bordering on surreal: the resemblance of a suspect who turns out to have been made up to Torgo from "Manos" The Hands of Fate becomes a major plot point.
- "One Watson, One Holmes" continues this trend; a suspect is lured into the open by Watson offering him a rare Thundarr the Barbarian lunchbox.
- In "Evidence of Things Not Seen", one of the murder victims is a female media expert named Sarkisian.
- "Tag, You're Me" sees Sherlock waking Joan up by holding a stereo over his head and blasting music, but apparently neither he nor Marcus has actually seen Say Anything... much to Joan's chagrin.
- An episode about the murder of a real-life superhero is titled "You've Got Me, Who's Got You?"
- Psych is referenced in "The Art of Sleights and Deception" when a suspect mentioned she called the police and spoke to a Detective Lassiter. Counts as a Take That!, given that her claims were not taken seriously.
- In "The Worms Crawl In, The Worms Crawl Out" Holmes and Bell are testing various bulletproof vests by having Bell fire his sidearm at them. Before firing Bell tells Holmes that he won't throw away his shot.
- In "Through the Fog," Sherlock and Joan are attempting to trim Clyde's nails, which Sherlock says are part of his natural defenses.Joan: Against what?Sherlock: Tomorrow never knows.
Shout Out / Elementary