Artistic License - Biology: Secret and Morocco use heat-sensor glasses to track down a chameleon villain. The problem? Lizards are ectothermic.
Berserk Button: Penny says it best herself; "Don't ever call me 'girlie.'"
The Cameo: 2 Stupid Dogs are two of the anthropomorphic guard dogs for the museum in "Chameleon". They also appear as their usual selves in "Scirocco Mole", along with Yogi Bear and Boo Boo. "Agent Penny" has an "Undercover Pub" peppered with portraits of Hanna-Barbera crimefighters as well as a cameo by Snooper and Blabber.
Reversing the situation, Secret and Morocco star in a dog biscuit ad featured in a Two Stupid Dogs segment.
Furry Confusion: ...played with. Nobody seems to have pets, but there is a Super Secret Zoo. The exhibits are in prison uniforms, making it more of a Super Secret Prison cunningly disguised as a Super Secret Zoo.
Getting Crap Past the Radar: In "Scirocco Mole", when Morocco, dressed as Scirocco, is walking through a bazaar, he bumps into a guy selling walnuts, causing his stand to fall down in front of him, spiling the nuts everywhere. The seller has his hands together on the spot of the stand next to his crotch and says, "My nuts".
Not to mention to the mole twins' origin story which go far back into the womb.
In "Platypus," a change ray switches the body parts of Secret Squirrel, Morocco and the Chief, with Secret getting Morocco's torso. In reaching in for what he thinks is one of his weapons, he instead takes out a magazine centerfold of a female mole.
"Chameleon" has the chief at an art museum exhibition heading up security (for what is presumed to be the last unstolen painting) and he asks a female patron if she'd be interested in "undercover work".
After being assaulted by One Ton with his own "Psychology in a can" spray, a dazed Secret Squirrel asks Morocco if his Freudian Slip is showing.
Half-Dressed Cartoon Animal: As in the original, but now hardly anybody wears pants, as Secret quite often demonstrates when pulling open his coat to deploy gadgetry. Being temporarily naked doesn't seem to be much of an issue, either.
Though Chief did seem to be quite embarrassed when it was revealed the bison wore bikini briefs.
And, oddly enough, Secret removes a pair of shorts when changing behind a screen in "Agent Penny".
Hollywood Darkness: Explained and lampshaded in "Dr. O," where the titular doctor cuts off all the lights in the world and blocks out the sun, leaving none of the characters able to see anything while the audience can still see them.
Narrator: "For the benefit of the viewing audience, a special filter will be applied so our fans may see all the action... in total darkness. Thank you."
In the episode "Agent Penny", he trades it for a variety of likewise indigo low-slung headgear.
In "Doctor O", he actually discards a smashed and broken hat...to reveal an identical replacement underneath.
When Morocco ends up wearing it in "Platypus", it's his nose which pokes through.
Non Sequitur Thud: In "One Ton", after the villain of the same name drops a desk on Secret using his Psychology in a Can against him, Morocco opens one of the drawers and Secret comes out, all bent out of shape, and he says, "Is my Freudian Slip showing?"
Portal Picture: The Chameleon loves to become one with great art. Secret causes him to have a breakdown by exposing him to modern, abstract works.
The Power of Hate: A rare heroic version—Secret counteracting Queen Bea's brainwashing Love Potion by channeling all his hate in order to save Penny from harm.
Puff of Logic: In Quark, Secret uses a dictionary to point out that quarks are a "hypothetical" subatomic particle, and makes the titular microscopic villain disappear.
A goof on Hanna-Barbera's part - by The Nineties, quarks had already been shown to exist. However, Secret could still disprove Quark: quarks are never found alone.
Pungeon Master: Secret is a constant stream of puns, and he's not alone.
Spot the Impostor: Played straight with Morocco and Scirocco Mole, each attempting to demonstrate that he's the bungling one.
Step into the Blinding Fight: In the episode with Dr. O where the lights are shut off, leaving Secret without the use of his sight to combat the Doctor's bat henchmen, who have no problems fighting in the dark. After taking some punches, Secret eventually focuses on using his other senses.
Vetinari Job Security: The plot of "Agent Penny". To save money, the Chief fires Secret, replaces him with Penny, and replaces Penny with Morocco. The result: Secret is bored out of his mind, Penny is a competent agent but gets tired of getting beaten up all the time, and Morocco destroys Penny's filing system by putting all the villains under "C" for criminal. Everyone is relieved when the Chief returns all the characters to their old jobs.
Villain of the Week: Aside from "Agent Penny", each episode had a different villain and was named after said villain.
And even "Agent Penny" wasn't a subversion of the trope.
Wacky Racing: "Hot Rodney", although with only two characters. Subverted: Secret cheats as much as the "bad guy" does, and ends up losing.
Then again, Secret only "cheated" in response to the bad guy's previous cheating and Hot Rodney crossed a line when he had a thug kidnap Morocco Mole just to force Secret to abandon a race.
We Meet Again: Though Dr. O appears in one episode, he and Secret Squirrel have meet many times before.
Wingding Eyes: The reflections on Morocco's shades often do this; the usual squiggle turning into an exclamation mark is a common one.
The standard squiggles are S-shaped. S.S. standing for Secret Squirrel, of course.
Or Super Secret.
World of Funny Animals: The revival is set in one. This is one of its biggest departures from the original series.
Would Hit a Girl: One Ton threw Secret Squirrel in drags. Though we're not sure if it's because he wasn't fooled one bit.