Fridge Brilliance: When Lee Jordan is introduced, he is shown piloting a red plane. Red is normally heroic, but who is most commonly associated with the color red in this series? And who does he join sides with (and eventually backstab)?
Foe Yay Shipping: Pairing Carmen with either Ivy or Zack isn't uncommon. It helps that Carmen is rather popular. It helps that Carmen isn't too malicious besides her thievery.
"Funny Aneurysm" Moment: Anytime the Chief lists three things and then says "Oh my!" becomes this when we learn the Wizard of Oz was Carmen's favorite series. Just think about it a little.
Ear Worm: If you can find another show featuring an epic sweeping adventure score merged with a jazzy gospel-esque choir set to a slightly altered piece by Wolfgang Amadeus Mozart as its opening theme, bring it.
Evil Is Sexy: Well, this IS Carmen Sandiego we're talking about.
Fanon Discontinuity: In most fan-fiction, the Player and anything referring to the show's universe as a PC game are largely ignored.
Genius Bonus: Some of the things Carmen tells the Player are either elaborations or paraphrases of quotes from fairly obscure philosophers.
Guilty Pleasure: When DVD Verdict reviewed the first season, the author wrote, "I'm guessing young kids will dig this, and older kids will find it a guilty pleasure..." This later became a blurb for the case of the complete series DVD.
Memetic Badass: Carmen is known for being both incredibly cool and incredibly skilled. She's the world's greatest thief after all.
Technology Marches On and/or Magic Floppy Disk: The Acme Detective Agency's entire database, Chief AI and all, can supposedly fit on a single standard CD. Granted, it was one of Carmen's own pieces of tech that pulled it off but still, she effectively stole Wikipedia and put it on a CD.
What an Idiot: At the end of The Tigress, Ivy reveals the whole thing was a set up to make Carmen jealous and cause her to let down her guard, so they can catch her. When they do, Zack explains how he made super powered rocket boots enabling Ivy to fly. RIGHT IN FRONT OF CARMEN WHO WAS HANDCUFFED NEXT TO HIM, enabling her to take the boots and fly right out of the police van! Did he suddenly forget who he was talking to?! He's a 14-year-old boy. Hormones do horrible things to teenagers' brains. Cut him some slack.
Mason Dixon's whole plan is to change history so that the Confederacy wins the Civil War and remains its own independent nation. As is pointed out in-episode, this will cause devastating changes to multiple other aspects of history that Dixon just isn't thinking ahead about.