Backup Twin: Kimmy the Geek is played by the same actor as Jimmy the Geek, a hacker friend of the Gunmen who was Killed Off for Real in an episode of The X-Files. Word of God confirms that Kimmy is indeed Jimmy's identical twin brother. It's been pointed out that even though the brothers share their hacking skills and relationship to the Gunmen, it quickly becomes apparent that their personalities are (subtly) very different, surprisingly somewhat averting Suspiciously Similar Substitute.
Book Dumb: Jimmy. He cleans computer keyboards with soap and water, puts used coffee filters through the shredder, and doesn't know "geography" from "geology", amongst other things. But he's also much more empathetic and in tune with human behaviour than the other Gunmen or even Yves, and sometimes this actually puts him one step ahead of the others.
Cliffhanger: "All About Yves," with the issues resolved on The X-Files "Jump the Shark" episode almost a year later. (Interestingly, the trio appeared a few times there before then - with the Season 9 premiere showing them immediately after their cliffhanger predicament.)
Descended Creator: Tom Braidwood was cast as Frohike while serving as an assistant director on The X-Files. Allegedly the casting director said, "We need Frohike to be your typical Dirty Old Man — like Braidwood over there."
Hollywood Spelling: No one ever asks Yves Adele Harlow just how that's spelled. The Gunmen discovered it was an alias, because it's an anagram of Lee Harvey Oswald. Her name was never spelled out until they made the connection, despite there being at least four different ways to spell the names involved. For one thing, 'Yves' is usually a men's name, and is pronounced exactly like the women's name 'Eve'.
Iron Buttmonkey: Jimmy takes a whole lot of crap, both from the writers and the other characters. He never complains.
Irony as They Are Cast: Three hackers working for Truth, Justice, and The American Way...played by three Canadians.
Jail Bake: Yves smuggles Jimmy an earpiece in prison inside a bag of Cheetos.
Information Wants to Be Free: Inverted in the episode "Like Water for Octane". The Gunmen are trying to find an experimental prototype water-powered car before an agent of an oil company, who presumably intends to destroy it. It turns out that the agent wants to see it mass-manufactured, and its original creator hid it away because he realized that freedom from oil would ultimately mean more cars and more consumption-his "miracle" would accelerate corporate devastation of the environment rather than stop it.
Shelly: It would mean more people driving cars, more people building places for people to go in those cars. More people, more consumption, more trees cut down, more roads laid in, and what do you pave roads with, by the way? Oil. The same oil you use to lubricate a water-powered car. The same oil that goes into all the plastics that make the tail-lights, the bumpers, the tires, just about everything else on the planet these days. And we'd have four hundred million cars on the road instead of two hundred million. Doesn't sound like utopia to me.
However, in every other case it's played straight and Up to Eleven. They are hackers and underground journalists who seek to expose "mundane" conspiracies and wrongdoings.
Prison Episode: "Maximum Byers," where Byers and Jimmy go undercover as prisoners for a case. The Fridge Logic of this approach was acknowledged In-Universe, as Yves asks why they didn't just dress up as prison guards.
Langley:(sheepishly) That's not how they did it on The A-Team.
Scully Box: The full-length photo of the five main actors used in promotional material quite clearly shows Tom Braidwood (Frohike) and Bruce Harwood (Byers) standing on one. Fortunately, the most commonly used version of the photo is usually cropped to only show the actors from the waist up; unfortunately, the full shot is used for the cover of the special edition comic book, and is veryobviously visible.
You All Meet in a Cell: As seen in in their origin episode on The X-Files "The Unusual Suspects," the three of them went into business together after getting tossed in jail during an unsuccessful attempt to expose a plot to test a mind control drug on unsuspecting asthma patients.