- The strip often makes reference to other newspaper comics, including Lampshade Hanging FoxTrot's perpetually-stuck-at-the-same-age style versus For Better or for Worse and its realtime progression.
- A few comics have featured background portraits with characters from other cartoons, such as Calvin And Hobbes, Dilbert, etc.
- Various Peanuts characters, including Charlie Brown, Linus, Lucy, and Snoopy, have actually made cameo appearances in the strip.
- One particular one has Jason and Marcus creating an identical snow sculpture of a snowman with a hole in his chest and a cannon right next to it to one in a Calvin and Hobbes strip - then creating sculptures of Calvin and Hobbes goofing around with the cannonball. "See, this way it's an homage, not a ripoff."
- Jason and Marcus often go to a store called Calvin's Hobbies
- There were also several references to several movies and TV shows in FoxTrot, namely The Matrix and Star Wars. In one strip, Jason also started paraphrasing Frasier Crane on Frasier (namely something about Le Fou Cheval restaurant switching to an all-domestic cheese list all while he is hosting a soiree at the restaurant to impress the membership chair of the chamber music board).
- One strip has Jason and Marcus acting out the famous 'quarter pounder' exchange from Pulp Fiction. This exchange was later referenced in another strip in an arc involving Jason attempting to take over Michael Eisner's position as CEO. Andy claims that Jason isn't even old enough to see some Disney films, with Peter thinking that he'll have them tamed down. Cut to Timon and Pumbaa, in the roles of Vincent Vega and Jules Winnefeld, respectively, holding guns with Timon stating "You know what they call a Water Buffalo with Cheese in the Pridelands?" and Pumbaa, who even went as far as to wear Winnefeld's afro, replying "They don't call it a Water Buffalo with Cheese?".
- In one strip, part of it is in a first-person perspective with an Aperture Science Handheld Portal Device. The person asks Paige, who is sitting at the computer, if they can get on to play Portal 2. She promptly tells the person to go away. A portal is shot above and below her as she then falls through. It then goes into a third-person perspective as you see Jason pointing a poorly made portal gun at Paige.
- A brutal, oafish football player is named Ogrynski.
- This Halloween strip has Marcus dressed as Mega Man X, while Eileen was Elastigirl, Phoebe was Hobbes, Eugene was Spock and Jason was Jabba the Hutt (although Jason's costume was part of the joke).
- Shout outs to Monty Python have appeared at least twice. In one strip Paige and Peter sport heads as swollen as Mr. Creosote's belly after cramming for math tests, with Jason offering them a "waffer theen" math formula.
- In another, Jason drew a flip-book of his sister being crushed by a 16 ton weight.
- Jason and Marcus once used toy soldiers to re-enact a scene from Saving Private Ryan (specifically the rallying scene to rescue him, although the beginning of the strip was a direct reference to when Miller first learns of his orders to retrieve Private Ryan). Jason's version either dealt with retrieving Ryan from a grill after he ended up melting before Roger used the grill.
- Another referenced Pearls Before Swine and its crazy rhyming here.
- The April 1st 2012 strip brought us A Game of Thrones, if sponsored by Hasbro. There have been two more A Game of Thrones jokes since.
- This one; most of the costumes are easy to identify, but Eilene's Hit Girl costume is rather obscure unless you've seen the movie.
- One strip features a Whole Plot Reference parody to Lewis Carroll's poem Jabberwocky, with the words changed to be about Andy making guacamole.
Shout Out / FoxTrot