Calvin, having an irrational panic attack in the 2009 episode "Invasion", claims that "Japan is going to fall into the ocean!" Two years later, a massive tsunami wrecked the country.
On a less serious note, the same episode has a brief bit lampshading the fact that Calvin has stayed six for a long time, with the MTM remarking that the writers would "think of something soon", since it was a sci-fi show. Much later, in The Collective, it's revealed that the floating timeline was the influence of the Chill Collective.
Then there's "SouthWest Pacific", which is about Calvin performing in a school play. What does the title mean, then? Well, during World War II there was an area entitled South West Pacific, where many important things happened. The wartime definition for this? A theater.
Also, the sequel's name, as proposed by Calvin, is Tornado Sharks 2: I Think Things Just Got a Little Windier. The sequel to Sharknadowill be named the equally stupid Sharknado 2: The Second One.
Irony: For all that Thunderstorm is more dangerous than Brainstorm, he's actually worse at the whole Mad Scientist thing than Brainstorm is. Brainstorm actually invents things (while Thunderstorm usually just imitates or steals Brainstorm's designs), and his failures leave himself and Earth alive for him to try again, while Thunderstorm's failure in Thunderstorm would have destroyed the planet, preventing him from ruling it (as well as likely killing him by throwing the satellite he was on out of its orbit).
Building on the above, Jack actually seems to be a more advanced AI than Shadow. He acts almost exactly like a human, has a distinctive personality, and even a sense of humor. Shadow merely serves Thunderstorm and attacks enemies, and, if it's not to help Thunderstorm, doesn't take initiative. He even gets a bit confused when faced with Jack while under orders to 'kill everyone' (Jack's a robot, and so not alive). Frankly, a scientist who was able to invent Jack would be more admired than one who could invent Shadow (and not just because people would be scared of Shadow).
Padding: Season 1 had a Running Gag where Hobbes would misinterpret something Calvin said or did, and Calvin would retort. The duo would then argue for a painfully long amount of time about something with no meaning to the plot. This has thankfully been phased out.note It should be noted that a similar chain of events was a Running Gag in the Hank the Cowdog series, which the author loves.
Painful Rhyme: Done intentionally with Calvin's love poem from "Insanity is in the Air":
The Woobie: Susie Derkins has the world against her in "Chains".
Dr Brainstorm in "Thunderstorm" considering he spent most of the movie trying to defeat his friend-turned-enemy who apparently betrayed him and rubbed his temporary victory in his face during the climax.
Socrates seems to be heading toward an arguable direction towards this in the final season.