Breaking the Fourth Wall: At least once. In the beginning of the series finale, the girls ask the viewer to wish them luck in their coming adventure.
Breast Expansion: In one episode, Alex takes a muscle-enhancement drug to defeat a villain, which also causes her breasts to visibly grow several times larger (Although at one point she did appear to have a completely masculine chest). Some also point out that the Art Evolution made the girls "powers" more obvious too (considering how fanservicey the show is… quite probable).
The Eighties: A villain has a ray that turns people a few years younger, and their clothes into 80s fashions.
Embarrassing Slide: In the episode "Shrinking", Jerry shows the Spies footage of various landmarks being shrunken and stolen around the world. In-between, however, is a clip of himself waterskiing and waving to the camera, to which Jerry reacts in the expected way.
Marco Lumière is a (more) unhinged version of Tim Burton.
This may also be a bit of the creators actually DOING the research, as the Lumière Brothers were the inventors of film over in France.
And Jerry strongly, strongly resembles Batman's butler Alfred Pennyworth as he appears in many comics depictions, particularly during the 70's — present (despite being more in the Bunny-Ears Lawyer side at times).
Fantastic Voyage Plot: In "The Yuck Factor", the Spies fought a trio of villains who tried to take over WOOHP from inside Jerry's brain.
Fiction 500: If not the girls, then at least the mother of the rival of the protagonists, who in one episode, buys an international chain of high-class boutique shoe stores in order to gain the last instance of a limited edition pair of boots.
Film Felons: At least once. Marco Lumière justifies this in being a batshit insane filmmaker.
Gladiator Games: In "Planet of the Hunks", an evil spoiled rich girl puts a handsome boy into her personal area to fight (or be killed) should she ever gets bored with him.
Gratuitous French: Clover has a habit of doing this, if only for the style. One episode reveals that, at most, her knowledge of French is pretty basic: she and Alex find an uncannily handsome pool cleaner guy who only speaks French. Every time he speaks, the girls get lulled about him (after all, Everything Sounds Sexier in French), but it's only with Jerry translating for them at the end that they know: all that he was talking about was the quality of the water in the swimming pool, and all that stuff (therefore, too technical for just Gratuitous French). Luckily enough for them, he had already switched to work for Mandy, whose comprehension of the language was about in the same level.
Highly Visible Spies: On their missions, the girls wear neon bright jumpsuits (even if they don't actually need to) and rarely make any attempt to hide or disguise their identities. Actual sneaking around, while not uncommon, happens about as often as barging headfirst into any objective. They aren't really spies in the traditional sense; it's more of a case of Not Wearing Tights.
Many episodes have them going undercover at whatever location they're investigating wearing clothes that fit the location and rarely, fake credentials if they can't get in by walking though the front door. They never actually hide their identity and often use their real first names as part of whatever fake identity they're using. It's only later once they break in to snoop around or after their cover is blown do they wear the highly visible suits.
The Movie reveals it was Clover who designed the outfits, before actually getting the gist of spying. To her credit, that's the most stealthy she could come up with (she also thought of superhero and Sailor Senshi outfits).
Identity Amnesia: In "Totally Dunzo", when Mandy goes into shock after breaking a nail, she has a different personality when she regains consciousness. She still knows who she is. The only difference is she's now a nice person.
"Oh it was easy! The manager of the arena has a cousin who lives next door to a guy who's best friends with a man who's married to a childhood classmate of a mother of a guy I know from the football team. I just flirted with him and he got the tickets for me."
Lampshade Hanging: "Is it me, or does the way we get Whooped sometimes defy the laws of physics?"
Taken to ridiculous lengths at the end of the Season 3 finale, "Evil Promotion Much?" After Terence is incarcerated, he rips off a mask revealing Jerry's face underneath. He then tells the guard watching him to release him with a very convincing acting. So is done. "Jerry" then knocks out the guard and tears off yet another mask which reveals that it was indeed Terence all along. In short, he was technically wearing his own face over a mask of Jerry with no prejudice to the features of "his own" face.
There's also the first half of "Escape from WOOHP Island" where Britney, while looking completely normal, was actually Willard in disguise. This was only found out when Clover's phony skin care products started melting "her" face. Granted, one of the girls notices that something's "different" about her, but you'd never have seen that coming.
Leitmotif: Anytime there's a beach or vacation setting, the same piece of music plays.
Life Drinker: The big bad uses some kind of magic stone to absorb youth from kids, resulting in this trope. As soon as aforementioned magic stone is destroyed, No Immortal Inertia is triggered.
Limited Social Circle: The only person Sam, Clover and Alex regularly interact with at their school (outside the three of them), is Mandy. Any other classmate they were seen talking to would be gone by the next episode, never to be seen or mentioned again (except for maybe the occasional boyfriend that would last about 2 or 3 episodes). Possibly justified in that their lives as spies would realistically get in the way of them having normal social lives.
Also the character of Arnold an example of Nerds Are Sexy (although he's rarely treated as much more than repulsive in-episode).
Male Gaze: About half the camera shots are focused on the girl's breasts as they are about to speak or when they crash into each other the camera is often focused their butts as they are lying on the floor.
One episode involves Tim luring the girls and their moms to a resort where he brainwashes the moms into offing them. With Clover and Alex's moms spending most of the episode in their bathing suits. If memory serves it culminates in a Mama Bear moment where the moms actually beat the crap out of Tim for menacing their little girls.
Also, in three-part episode "Totally Busted", it was revealed that the protagonists' crazy skills came from having a special set of "spy genes" which they inherited from their mothers. As the episode progressed the Spies were brainwashed and their mothers are recruited to save them. This result in Mama Bears in Catsuits
Mistaken for Badass: In "Evil Coffee Shop Much?", Jerry hires Mandy as a spy because he thinks she somehow snuck into WHOOP HQ when in actuality she was just accidentally WHOOP'd along with the main girls and fell behind the couch.
No Celebrities Were Harmed: This show was particularly bad with this. In fact, one episode centered around a number of knockoffs of Bill Gates, Oprah Winfrey, Britney Spears, etc., and the villain was Milan Stilton.
On Three: In "A Spy is Born Part 2", Sam tells Clover and Jerry to open the door on three. Clover asks if they should wait for "Go". Sam is annoyed and clarifies: "Three! Who said anything about "go"?!"
Paper-Thin Disguise: Wanted criminal Tim Scam was able to pretty much take over WOOHP by using an alias that was literally just his name backwards. And he had it clearly written on a name badge just in case there was a slight chance no-one would figure it out.
References to Sailor Moon are probably an inside joke, as at least one of the voice actors — namely Katie Griffin, who plays Alex — also voiced Raye in the early DiC-dubbed episodes of that show.
Charlie's Angels, when a villain impersonating Jerry accidentally calls Alex "Farrah".
WOOHP sounds suspiciously similar to WOOC(P), the employer of the protagonist of The Ipcress File and other Len Deighton novels.
There is a Shout Out to Tsukasa Hojo's Cat's Eye in EVERY SINGLE EPISODE. More precisely, the tomboyish brunette Action Girl with a yellow Spy Catsuit Alex is an Expy for Ai Kisugi, the youngest of the three sisters. It's much easier for the French viewers to figure it out, since Ai was named Alex (short for Alexia) in the French dub. It also helps that Cat's Eye was broadcast multiple times on French public channels in the '80s (and well beloved). And yes, it was displayed on kids programs. Which the creators of the show grew up watching. Explains a lot, doesn't it?
In the episode "Spies Vs. Spies", the agents whom predate the girls, Pam, Alice, and Crimson, seemed to have been directly modeled after the girls from Cat's Eye.
Crimson is a reference to the rock song "Crimson and Clover"
Also, whenever the girls are shown playing soccer, the animation draws much inspiration from Captain Tsubasa, from the balls taking on an oval shape after being kicked, all the way the ball spinning in the goalkeeper's hands until his gloves are fizzled out. Especially if Alex (who is a professed soccer fan, as per "Spy Soccer") is involved.
In the episode "Miss Spirit Fingers", Alex and Clover have a blink-and-you'll-miss-it moment where they crash into a Pulp Fiction poster.
Jerry's Matrix-style jump to the helicopter in the episode "A Spy Is Born (part II)".
And there's another possible Matrix reference in the series 2 episode "It's How You Play the Game" with the wriggly silverfish robots used to infect people's minds by the Big Bad. They go in through the ear, though, not the belly button.
Oooh! And the James Bond crotch-laser in the episode "Starstruck".
Also when Jerry's mother, in a flashback, rises from the sea in an orange bikini with a white belt.
King Kong, when the gorilla climbs up a skyscraper with Alex on its back in the episode "Animal World".
Averted with GLADIS. Despite what many would think, this show's GLADIS actually came first.
But GLADIS' main interface looks a lot like Shirka from Ulysses 31.
Something Completely Different: "Matchmaker" is one of the few episodes not to feature Jerry summoning the girls to WOOHP for a new mission. It's also one of the few where Clover solo has to save the day.
Spin-Off: The Amazing Spiez, which is more like a continuation of TS with a younger cast. Sam, Clover and Alex make an appearance in one episode.
Spoiled Sweet: Sam, Clover and Alex, the latter being a straight-up example.
Temporary Love Interest: Practically every episode gives at least one of the girls one. And every time one of them actually gets with a guy they're right back to being single by the next episode due to one of the following reasons:
He turned out to be a villain.
He dumped her or she dumped him for some superficial reason (or not).
Temporary Bulk Change: Clover along with a great number of others put on several hundred pounds over the course of a few days from eating Passion Patties.
Scratch that. Clover and Jerry put on that much over the course of a day!
Bittersweet put on that much in a few seconds after being forcefed her concentrated additive.
Time Travel: By now about 3 different methods are readily available to the team.
Timey-Wimey Ball: In one of the early episodes the girls are sent back in time to the dark ages. Clover is, at least for a little bit, able to hail Jerry on her communicator despite him not being born for hundreds of years.