Awesome Music: 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.
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 and isn't too malicious besides her thievery (not to mention very protective of her rivals).
"Funny Aneurysm" Moment: Anytime the Chief lists three things and then says "Oh my!" becomes this when we learn that The Wizard of Oz was Carmen's favorite childhood story. Just think about it a little.
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.
The "Retribution" story arc involves Dr. Maelstrom attempting to steal the RMS Titanic and later, Noah's Ark. At the end of the first arc, The Chief mentions that Real Life underwater explorer Robert Ballard discovered the Titanic shortly after Maelstrom's capture. A few years after the episode aired, Ballard would go on several expeditions inspired by the story of Noah's Ark, and would later be very vocal in his opposition to removing artifacts from the Titanic. If the episode had aired ten years later, it might have seemed as though Maelstrom was intended to literally be Ballard's Evil Counterpart!
Magnificent Bastard: Carmen herself, of course, but much later in the show, we also get Dr. Maelstrom.
Memetic Badass: Carmen is known for being both incredibly cool and incredibly skilled. She's the world's greatest thief, after all.
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 that they could catch her. When they do, Zack explains how he made super-powered rocket boots enabling Ivy to fly, right in front of Carmen who is 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? Although perhaps this was the result of his hormones doing horrible things to his brain.
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.