Eye-Obscuring Hat: Subverted by Secret Squirrel, whose hat brim almost touches his nose, but has two eye holes so that he can see.
Funny Animal: Both Secret Squirrel and Morocco Mole, as well as a few others.
Hey, It's That Voice!: With Mel Blanc as the voice of Secret Squirrel, it's no surprise that he sounds like Sylvester in the early episodes, then later like Heathcliff with a lisp! Paul Frees, voice of Morocco Mole and their long suffering Chief Double Q, also provides plenty of voices in addition to Blanc, even using his Boris Badenov voice (of Rocky and Bullwinkle fame) for villains like Yellow Pinky!
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: 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.
In 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.
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.
The Cameo: Two 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.