In the "Cross my Heart Job", Hardison, undercover as a tower operator, uses the callsign "Leverage Airlines 1701" to when radioing the team's walkie-talkies.
The team's aliases have a tendency to reference Doctor Who; given that Hardison presumably arranges all their fake IDs and is canonically a fan, this is almost certainly no coincidence even in-universe.
Hardison misses the beginning of the job in "The Mile High Job" because he's been up all night playing World of Warcraft - and cries "for the horde!" when he meets an employee of the evil corporation of the week who's also a fan.
In "The Two-Horse Job", Parker's disdain for horses stems from an incident that happened in Camden, IL (Beth Riesgraf is Jason Lee's baby-mama, and has made a few appearances on the show).
In "The Two Live Crew Job", Wil Wheaton guest-stars. His hacker handle is "Cha0s", and the CIA calls him "The Kobayashi Maru". Before you start raising questions, just assume that Wesley Crusher was not played by Wheaton in the Leverage universe. Or even better, never existed at all.
Alternately, if you accept the tie-in novel The Con Job as canon, Wheaton and Cha0s both exist, independently of each other.
In "The Juror #6 Job", the bad guys' jury-monitoring setup strongly resembles the one in Runaway Jury.
In The "Order 23 Job" Hardison and Eliot are Officers Michaels and Crichton. (Michael Crichton is well known for his Medical Thrillers and helping create ER; he also wrote The Andromeda Strain, about a virulent disease that traps the main characters in a medical facility...)
In that same episode, Hardison sets up a system with Eliot of referencing the odd-numbered Star Trek movies when things are going well and the even-numbered ones when things are going poorly. Eliot later uses a similar system to get Hardison's attention by paging "Kirk Picard" in "The Cross My Heart Job."
In "The Reunion Job", Parker claims to have overheard a bunch of ladies saying that Drake McIntyre (who Nate was impersonating) was "the best they ever had".
In "The Inside Job", Parker gets into trouble when she tries to break into a building with a "Steranko" security system.note Jim Steranko, a comic artist, was perhaps most famous for his "Nick Fury: Agent of SHIELD" work. Nick Fury was a counter-intelligence expert, so "Steranko" is an apropos name for a security system. Steranko was also an escape artist before working in comics, so giving his name to an escape-proof system is a bit of intentional irony. Also, Sophie and Hardison give the aliases Emily Peel and Jonathan Steed when pretending to be auditors. And we're introduced to Archie Leach - "the greatest thief of all time".
The security chief in "The Inside Job," portrayed as a ruthless killer, is named Mr. Voorhees.
In "The Boost Job" Hardison readies an EMP device that makes the same noise as a proton pack. He then lampshades it by adding "this chick is toast", which is Bill Murray's line when the team confronts Gozer. Later in the episode, when Hardison and Parker enter a chop shop and find that it's a much bigger operation than they expected, he remarks "We're gonna need a bigger boat".
According to Word Of God it's inspired by a The Saint story but he wouldn't say which one. More than one commenter on John Rogers' blog thinks he's talking about "The Wonderful War".
A number of staff shout-outs:
The team frequently runs into "Glenn-Reider" safes - named after the show's "Wonder Twin" writers Melissa Glenn and Jessica Reider.
The building on the docks in the "Three Strikes Job" is called Kirsch Industries, after writer's assistant and occasional episode writer Rebecca Kirsch.
You can see candidate posters in the background of the campaign office in "The Jailhouse Job" for writers Scott Veach (who's running for city council), Charlotte Boylan (who's running for Congress), and Geoffrey Thorne (who's running for county sheriff).
Eric Stoltz's character in "The Long Way Down Job" is named Alan Scott.
"The 10 L'il Grifters Job" includes shout-outs to all manner of detective stories:
The title is a reference to Agatha Christie's "Ten Little Indians," and the story plays out much like a classic Christie story.
Nate is dressed up as Ellery Queen - which also serves as an Actor Allusion, since in the TV series Queen was played by Timothy Hutton's father Jim. Nate is also trapped in a room, and requires everyone else to do the legwork; this makes the story a Nero Wolfe style mystery, but with Hutton as Wolfe, rather than his Sidekick Archie Goodwin (whom Hutton played in A Nero Wolfe Mystery).
Eliot is Charlie Siringo, a real-life Pinkerton Detective. A more subtle reference than most of the others — Pinkertons became nationally famous for protecting then President-Elect Abraham Lincoln and later being hired by the U.S. Government when the Department of Justice didn't have the ability to pull off a huge investigation, after originally working mostly for the railroad corporations.
Eliot himself is practically a shout-out to the Spenser novels.
As they enter a disorganized evidence room, Hardison asks Parker if she thinks they'll find the Ark of the Covenant.
In the "Cross My Heart Job", in order to get Hardison's attention, Eliot has the airport page for a "KirkPicard", which is also a Call Back to "The Order 23 Job," in which Hardison pages "Dr. Ralph O'Khan" to let Eliot know he's in danger.
The heart of the title is stolen by a wealthy, greedy, isolated old man. Nate gives him a snow globe instead.
In the "Maltese Falcon Job", when threatening the mayor, Nate refers to Hardison, who is to be the one putting the hurt on the mayor as Mr. Joshua, Gary Busey's role in the first Lethal Weapon.
The jerkass frat boy — sorry, "Dustman" — in charge of a CIA torture experiment in "The Experimental Job" is named Zilgram, possibly a portmanteau of Zimbardo and Milgram. Parker later has fun with an "actual" Milgram experiment (girl loves her electricity). Sophie and the lesbianFair Cop in the same episode might be a reference to Rizzoli & Isles.
In "The Gold Job", while following clues the Leverage team has planted, one of the marks talks about ciphers and how they sometimes use they text of a well-known document, such as the Declaration of Independence.
In the same episode, Hardison interacts with a computer named GLaDOS.
In "The Last Dam Job", the gang's new headquarters is explicitly compared to the Batcave, and Eliot seems to quite like the idea of having an "Eliot Signal".
Quinn quotes Tombstone to Eliot, who grins and responds "I love that movie!"
Sophie also gets a bunch of actors to wear Value More uniform and pose as fake workers, much like an Improv Everywhere mission only with more malice.
The entire episode "The White Rabbit Job" is one long shout out to Alice in Wonderland: the mark's name is Charles Dodgson, his second in command is named Mr. Carroll, and one of his employees (the one who hires the Leverage team) is named Alex Liddell.
The Matrix: Hardison makes his dream world using CGI screens; Dodgson is dosed with red (woozy) and blue (knock-out) patches and is convinced he's in a dream when Sophie makes a shiny metal ball float (Neo sees a boy bend a shiny metal spoon and other kids make toys float).
Inception: The team is pretending to hack into Dodgson's brain and change his personality at the behest of someone else; Dodgson had issues with his greedy, hard-ass dad; Sophie claimed to have done the "impossible con" but actually lied, the opposite of Cobb who claimed inception was impossible but had done it to his own wife; Dodgson is "haunted" by the death of his cousin to the point where he's destroying his career, his life, and the lives of everyone around him.
A few of the shots are very Inception-esque—like the shot of the staircase from the top, very much like the 'Pendleton steps' shot in Inception.
The plot of Inception was to convince a man to split up his family's business; the plot of "The White Rabbit Job" is to convince a man to keep running it.
Eliot yelling at Hardison about his lack of research —> Dom yelling at Arthur about his lack of resarch.
Paprika: Sophie poses as a "guided dream therapist" who appears in Dodgson's "dreams" to help him with his problems; towards the end the dreamworld con collapses and Dodgson has no idea what's real or fake.
Dodgson makes an appearance dressed like Steve Jobs — blue jeans, black turtleneck with rolled-up sleeves, headset microphone, and Perma Stubble.
The very last Shout Out in the series comes when Hardison outlines his plans for the future: "Leverage International" (which is obviously inspired by Batman, Inc.)
Keeping in style, one last Doctor Who reference: Parker's alias is Detective Tennant.
Way back in the pilot, in a Freeze-Frame Bonus, when they're breaking into Pierson's server room, it shows the screen of the skimmer Hardison used to crack the code. The first seven numbers are 8675309.
The Phony Psychic in The Future Job is named Dalton Rand - his surname is a reference to the infamous psychic (who later became a notorious skeptic and debunker of phony psychics) James Randi.
Hardison, playing a vintner for a con in "The Corkscrew Job", christens himself The Grape Gatsby.