The Great Hogwarts Noodle Incident, the details of which are never revealed in Dangerverse canon, and which, according to Remus, "all started with a comic book, an action figure, and a stuffed tiger…" According to Word of God, the comic book and action figure are Stupendous Man and Spaceman Spiff, respectively.
Justice League of Equestria"; one of the side stories to Mare of Steel'' has Rainbow Dash playing superhero as a child, complete with her arch nemesis "Mom Lady" and introducing herself as "Defender of Cloudsdale, foe of Tyranny!"
FoxTrot has a few references, such as this dialogue:
Peter: [after an incredibly lame pun by Jason in the style of Pearls Before Swine] Remind me to start hiding your Pearls Before Swine books. Jason: You still haven't returned my Calvin and Hobbes books after the Noodle Incident, by the way.
A couple strips have background characters with Calvin's distinctive hairstyle.
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.
Hobbes is also among the imaginary friends shown here.
In a One Big Happy strip, Ruthie and Joe are supposedly about to travel back in time, when Ruthie comments about the food they packed, "Won't the popcorn turn into corn on the cob, then into corn stalks? And the orange juice will turn into oranges before our very eyes!" Joe then comments that he would have been better off with a stuffed tiger as his copilot.
One Garfield title panel has several newspaper comic characters trick-or-treating, Calvin being among them.
The black panther monster has an attack where it pounces on you, ending with the phrase "Homicidal psycho jungle cat!"
The description of the War Frat Mobile Grill Unit has this:
Oh, and look — there's a sticker on the back window with some cartoon character peeing on something. Now *that's* unexpected.
One adventure has the option to get meat from a hobo by telling him it's Opposite Day, and that you declared it oppositely by not declaring it, much like an exchange between Calvin and Hobbes.
The "cheap toaster" item has a description containing a joke from one strip:
This is a cheap toaster. You put bread in it, push down the lever, and in a couple of minutes, toast comes out! Nobody knows where the bread goes.
The "pair of eXtreme mittens" remarks on the player's "lack of razor-sharp claws", much like Hobbes said in one strip.
One strip has Calvin finding a secret decoder ring, joyfully declaring that he and Hobbes can communicate to each other without their parents understanding, then realizes that they probably can't understand him normally anyway. This is given homage in the description of the encoder ring item:
Now you can send secret messages to your friends that will look like complete gibberish to everyone else. Assuming, of course, that that wasn't already the case anyway.
The Mad Hatrack familiar quotes Tracer Bullet: "I have three slugs in me. One's made of lead, and two are made of bourbon."
The funny paper hat describes several different comic strips, ending with "Whew, thank god for the lunatic kid who thinks his stuffed animal's alive."
In Homestar Runner's long-awaited 2014 Halloween toon, The Cheat dresses as Calvin's sci-fi alter ego Spaceman Spiff.