Big Bad Friend: Humpty was the Big Bad the entire time. Although later in the movie, he redeemed himself and was on Puss' side again.
Bilingual Bonus: Many, as the movie is set in an AU! Spain. Yet this one takes the prize:
Puss (Referring to Humpty Dumpty): Maldito huevo...
Literally, "Damned egg". Made even better by the fact that huevo is also used as an euphemism for testicle.
You also get a relatively rare occasion in which the phrase "Holy frijoles!" - often used in a stereotypical fashion in film and TV depictions of Mexicans, or used by non-Mexicans as a generic exclamation in the same context as "Aye Cayrumba!" - is actually uttered by a noted Hispanic actor in a non-stereotypical context.
Dance of Romance: Subverted in Puss and Kitty's first "dance" due to Puss being unaware his opponent is female; played straighter in their dance after retrieving the Golden Goose, which is much more intimate.
Face-Heel Turn: Humpty gets a bit too into his dream of finding the golden eggs, and what once began as an innocent dream turns into an unhealthy obsession when he grows older. Enough for the Reveal in the movie to be that Humpty orchestrated the whole plot, thereby turning Puss into the outlaw once again. However, later in the movie after Puss is angry at him for betraying him, he becomes Puss' friend again and even tries to help him out at the end.
Flashback: A lengthy one is given by Puss to explain to Kitty (and the audience) the extent of his relationship with Humpty Dumpty.
Foregone Conclusion: Anybody who has been on the Shrek 4D ride at Universal Studios would have seen Humpty Dumpty's apparent death coming, as Donkey accidentally knocks over his grave marker in the cemetary scene.
Foreshadowing: Humpty Dumpty, upon finding the Golden Goose's "nest", remarks that he feels like he belongs there, and later remarks that he didn't feel like he belonged in San Ricardo much less anywhere. He turns out to be a golden egg given life.
Also, when Jack and Jill say that "it's their cue" after finding Humpty's telescope, things feel like Humpty was the one responsible for the whole thing.
Furry Reminder: Similar to the previous movies, while Puss is more or less a swashbuckling hero, he can't overcome his feline instincts.
Gambit Roulette: EVERY event up to the climax at San Ricardo was Humpty's gambit for revenge.
Genre Shift: The regular Shrek series was an Affectionate Parody of fairy tales, a trait that's prevalent even through its most serious moments. Puss' story in the 'verse keeps the irreverent sense of fairy tale humor (in a lesser amount) but has a much more action-orientated tone similar to Pirates of the Caribbean.
Getting Crap Past the Radar: The opening scene has Puss grabbing his stuff and getting ready to leave this sleeping kitty in the morning. Apparently he only did that to steal her owner's ring, which adds fresh implications.
Puss has quite the reputation with the ladies. Apparently, he's called "Mr. Friskie Two-Times".
This line from Humpty:
Humpty Dumpty: Do you know what they do to eggs in San Ricardo Prison? I'll tell you this much.... it ain't over easy.
Getting even more past the radar, if it ain't over easy? Guess what it is - sunny side up. Yikes.
A cat walks into a bar and orders milk. Whereas the humans are drinking from actual beer bottles. Or are they?
The prison guard seemed pretty put-out to find Puss carrying catnip. Knowing how cats react to the stuff...
He says it's for his glaucoma, for which medical marijuana is sometimes prescribed.
Kitty Softpaws' costume includes a little kitty cat gimp mask.
Really, with a film focusing on a character like Puss, most of the one-liners are pretty much this.
Puss in prison starts to clean himself—the way cats do—until he realizes he's being watched by an apparently perverted old man....
When Humpty Dumpty first appears, Puss says "Maldito huevo," which translates as "Damn egg."
One of the lowlifes in the bar tells the story of the legendary Golden Eggs, via his various tattoos. Then he reaches for his pants, asking if Puss would 'like to see the eggs'.
Gory Discretion Shot: Subverted. Jack and Jill slam Humpty against a wooden cart by their shadows on a wall, then a crack sound is heard and liquid starts spraying out of Humpty. Turns out it's just a champange bottle.
Hollywood Density: Averted; the golden eggs turn out to be so heavy even taking one would have been difficult. That said, the characters do occasionally handle them as if they were far lighter, but this is more artistic than plot-relevant.
Humpty seems to be no heavier than he looks, however, despite it being revealed at the end that he is a golden egg, and quite a bit larger than any of the other ones. Dude should have weighed a couple hundred pounds, but the cats have no problem helping him up or rolling him around.
Hypocritical Humor: Puss takes offense at Kitty doing the "litterbox" (a kicking-sand motion with her hind legs) at him, only to turn around and drag his butt on the floor as an equally offensive comeback.
Impossible Thief: Kitty. A Running Gag has her steal Puss' hat and boots without him noticing until she points it out. Puss later gets to do this to some guards by making their pants fall down without apparently moving a muscle.
Improvised Weapon: Puss uses a guitar to knock Kitty out in their first duel, revealing her identity.
In Love with the Mark: Kitty slowly falls in love with Puss over the course of the adventure, despite being in on Humpty's revenge scheme. Thus, she busts him out of jail and helps him save the city in the end. Humpty, to his credit, is Genre Savvy enough to catch on and tries to cock-block, but doesn't do a very good job.
Jump Scare: A minor one when Humpty says, "Hi, plant" to the little sprout in the desert.
Kirk's Rock: The trio pass in front of a creditable rendered version at one point.
Kissing Discretion Shot: Finally, after all the UST between the two, Kitty and Puss finally kiss. Which is hidden behind Puss's hat which Kitty lifts off his head and holds over their faces. Likely done just the give the two some privacy, though they hadn't really been discreet about their attraction before. Could also count as a (covered up) The Big Damn Kiss, because of the dramatic lighting behind them.
Mating Dance: There is a quite passionate and fast paced one between Kitty and Puss after they retrieve the golden chick from the castle, they literally can barely keep their hands(/paws) off each other! Complete with with a Almost Kiss and even a Held Gaze moment.
The "Dance Battle" can be interpreted as this, if one-sided.
Meaningful Name: Kitty Softpaws can rob you blind and literally has no claws.
Meet Cute: Despite the fact they were (so it seemed) preparing to fight to the death (and the fact guitar clubbing was included), the first real time Kitty and Puss meet, they seem to have easily over looked that fact, and Puss later expresses his regret over the guitar.
Puss again puts on his Puppy-Dog Eyes, this time for a prison guard so he may escape. The score during this part is the same melody played during the first time Puss does it in Shrek 2. It's even on his Wanted poster.
Never Live It Down: In-universe. Kitty keeps reminding Puss he hit her in the head with a guitar.
Nice Hat: Puss has a Musketeer-esque hat, complete with feather.
Revenge: Humpty's entire plan was to lead Puss back to San Ricardo so he could be locked up (as revenge for "betraying" him), and to also lead the Golden Goose's mother there to destroy the whole town (as revenge for locking him up).
Revenge Myopia: Humpty's big grievance against Puss is the fact that Puss abandoned him to the authorities after the failed robbery of the bank. Humpty seems unwilling to recognize that he is just as guilty by tricking Puss into aiding him against his explicit wishes, and ruined his hard-earned reputation as the town hero in the process. He doesn't even view what he did as a betrayal, thinking that Puss was just supposed to go along with it because they're blood-brothers.
Samus Is a Girl: Kitty, who for the first few minutes of her appearance wears a heavy black mask to hide her face. Given the generally realistic cat proportions the only real thing marking her as a different gender anyway is her voice (at least to the audience. Puss has no problem telling by her face, even though he seems incapable of identifying a female cat otherwise, apparently).
The Mother Goose's attack on San Ricardo is very similar to the 1997 Tri Star Godzilla, right down to the final assault on the bridge(and her attacking Humpty's plane from below, just how 'Zilla chomped a helicopter in the movie).
"His boots are made of soft Corinthian Leather" is a reference to Ricardo Montalban (one of the most prominent Hispanic actors in early Hollywood) and his famously suave endorsements for Chrysler. Montalban also co-starred with Banderas in one of the Spy Kids films, and it's very likely "San Ricardo" is named in his honor.
Jack and Jill's little ones are ten little piggies.
Humpty at one point tightens his golden suit so that only his eyes are showing, and starts mumbling in an incomprehensible way. Kenny, anyone?
Signature Style: Despite Guillermo Del Toro merely producing, a couple of his trademarks like Steam Punk (Jack and Jill's cannon carriage, Humpty's transforming carriage) and fantastically improbable creatures (the mother goose) appear in this movie. Not to mention that it's the first work since Pan's Labyrinth that's set in a remotely Hispanic setting.
So Proud of You: Imelda says this to Puss after he saves San Ricardo from the golden goose's mother.
Spexico: San Ricardo and it's surroundings are the definitive Spexico. Considering that Puss originated in the Shrek movies, which seem to take place in Arthurian Europe, one would presume Puss is Spanish. San Ricardo and it's surroundings, however... ain't exactly medieval Spain.
Then again, weren't a lot of classic Westerns filmed in Spain (standing in as Western US/Mexico)?
While Puss was pursuing Kitty, he went trought a house and a woman began yelling "EL CHUPACABRAS!" El chupacabras leyend is only from latin America, not Spain.
Steampunk: Jack and jill's wagon-cannons, Humpty's glider-wagon.
Swallow the Key: Jack swallows the key that locks the box where the magic beans are kept.
Taken for Granite: According to Humpty, anyone who looks at the monster in the castle will turn to stone. This is a lie and is only meant to keep Puss and Kitty from finding out that the monster is the Goose's mother.
Puss's Overly-Long Gag with sipping the leche. ...he still does it in the actual movie, but it's no longer a long gag, and he doesn't say, "I'm still thirsty" after finishing.
The running gag with the cat that goes "Ooh...!" has him taking his hand out of his mouth after Puss scolds him, which doesn't happen in the actual movie.
True Companions: Puss and Humpty, when they were kids, and considered each other "brothers". Not so much in the present, though Humpty tries to get it back or at least pretends to, in order to take revenge. However, Puss manages to appeal to the good still in him, and they seem to be friends again right before Humpty's death.
What Measure Is a Non-Cute?: The adorable Puss is praised as a hero and loved like a son by the orphanage matron while his childhood friend Humpty, who is pretty much just a big face, is regularly mocked, gets into much trouble, and is the true antagonist of the film.
Where It All Began: The story eventually leads back to Puss' hometown of San Ricardo. Of course, this turns out to be intentional, as part of Humpty's revenge plot.
Who's Laughing Now?: Invoked word for word (barring the accent) when the castle in the clouds is proven to be real.