Brick Joke: In Chapter 7, Evil Calvin complains about the quality of a certain vendor's chocolate ice cream, planning to sue. Later, in Chapter 13, he asks Fake Mom and Fake Dad for some chocolate ice cream - specifically better than the vendor's. (He's still planning to sue, too.)
An early chapter has Sherman biting Socrates' ear. In Chapter 13, Sherman responds to a disparaging remark of his with "Come closer so that I may bite you," prompting Socrates to back away and rub his ear.
Another early chapter has Calvin playing mock-Jeopardy! with an alien. Much later, in Chapter 14, an alien responds to a question with "I'll take weird creature for 500, please."
Chekhov's Gun: After Socrates uses the Time Pauser, Andy pockets it for safekeeping. Later, in Chapter 13, he and Sherman flee from some guards and end up activating it.
Sherman: Well, well. It would appear that your inability to remember anything has paid off.
Better yet, the very first chapter has Calvin using the Time Pauser to extend summer vacation, and Hobbes asks "what happens when you touch the button again, but I'm not touching you? Do I stay here in the point where time doesn't exist?" Seventeen chapters later, Hobbes remembers this moment and comes up with a plan to trap the villains in paused time forever.
The original "gun" comes up again, as Andy apparently dropped it - leading Retro to get it.
Another incredibly long wait between reappearances: the guitar used in the climax of Calvin and Hobbes: The Movie is used again to get Calvin out of a force field.
The gun used at the end of Trouble Island (helpfully pointed out by the narration) is used again to revert things back the way they were.
Circling Birdies: After getting socked by the evil Calvin, Hobbes sees "a bunch of stars, planets, tweety birds and somewhere in the deeper recesses of his brain, he heard a harp playing for no apparent reason."
Double Subversion: When Socrates finally learns about his transmitter chip, he marches over to Sherman, plucks him up, and... begins laughing. After everyone else starts laughing, he abruptly stops and angrily tells him to take it out.
Duck Season, Rabbit Season: Retro does this with Calvin when they're arguing over whether the former is Rupert in disguise or the actual Retro.
Rupert:Next time, Next time, we don't just go bursting into people's homes like we did. We freaked everyone out. Earl: Isn't that a good thing? Rupert: Normally, yes, but it's not when they throw their furniture at us and yell "GET OUT, GET OUT".
Group Hug: Socrates asks for one as a Last Request - allowing him to use the Time Pauser and get out of Dodge.
Ha Ha Ha No: Socrates' reaction to Sherman suggesting he'll let the whole transmitter chip thing slide.
Hates Being Touched: Bob immediately zooms away upon realizing Earl's about to touch him during their conversation.
Insignificant Little Blue Planet: The planet selector's explanation of Earth is "home to the most obsolete and stupidest aliens in the universe, THE EARTHLINGS!" Calvin argues against it, but the voice simply tells him that they're always fighting and have never visited another planet. He can't argue with that.
Susie: Man, you are evil! Evil Calvin: Why, thank you.
Ironic Echo: Evil Calvin threatens a man that he'll be beaten senseless on the count of three. Later, when he holds the remote to destroy the Earth, he does the same thing - only everyone bows down before "three".
Kill and Replace: Retro's plan for Calvin is to kidnap him, ruin his reputation with an evil clone, lower defense systems so the aliens can take over, and then kill the real Calvin.
Kill It with Fire: Hobbes tries this on the Shadowfax, but it doesn't work - the Spacers are weak to fire, and the Shadowfax actually love it.
Kill It with Ice: The actual weakness of the Shadowfax, which Socrates exploits with a catch rope and a freezer.
Kill It with Water: Hobbes tries this on the Shadowfax, but it doesn't work - it was actually the Blackosts that were weak to water.
Nebular: The fact that nobody seems to know that Calvin is the Supreme Earth Potentate. Plus, the fact that a six-year-old boy is the leader of a planet is also a bit odd. Galaxoid: And then there's the fact that he is constantly denying that he is the Earth leader.
Last Request: Evil Calvin lets Socrates have his - a Group Hug, which allows him to use the Time Pauser and save everyone.
Your Princess Is in Another Castle: The protagonists have finally gotten Rupert, Earl, and Retro out of the way, the alien crew is happy, and they all return home. It all seems well until you remember there was another threat back on Earth...