This image◊ is at least worth a chuckle, even if it doesn't make you crack up— but it's more likely to inspire the latter reaction. (And a bonus! The image itself is spoiler-free!)
End of the movie laughs: to avoid having Perry reassigned, they use Doof's Amnesianator to wipe everyone's memories of, as Phineas calls it "the best day ever." Just before Major M pulls the switch, Isabella double checks to make sure that its as going to wipe their minds of the entire day. Cue Isabella planting a kiss on Phineas. Her smug as hell expression after the fact only adds to the hilarity.
The funniest part of that: Phineas knows Ferb has his hand up without even looking, implying that he already knows about Ferb's double life. Makes you wonder what kind of double life Ferb could have that Phineas not only knows about, but is completely unfazed by.
Doof-2:(chucks muffin at Norm's head) YOU'RE BROKEN!
After the gang escape into A Brand New Reality, Doof-2 decides to invade their dimension.
Doof-2: ...And someone get me another muffin!
Normbot: But it's not Muffin Time!
Agent P manages to distract Doof-2 for a few seconds by transmitting an image of naked Monogram. Major Squick ensues.
Monogram's in the shower, and the chain-reaction - Doof-1 covers his eyes, then Doof-2, then Platyborg, then the Normbots - is icing on the cake. Apparently a bubble-clad Monogram is Brain Bleach material.
"I told you! Not between 3:30 and 4:00!"
Doof-2's reason for being even more evil than our Doof: he lost his toy train as a child. Even our Doof can't follow the logic.
Doof-2 was himself surprised that our Doof didn't become as evil as he is due to his many Freudian Excuses.
Granted, this moment being in the middle of a fairly serious situation kind of diminishes it, but Doofenshmirtz realizing that Perry deliberately peed on his couch has got to count. Especially considering Perry's face at the accusation.
And of course, Doofenshmirtz's complete inability to recognize Agent P without his hat. Doof-2 had already spent a couple minutes trying to point this out to him, and eventually decides to have Platyborg attack Phineas and Ferb to force Perry to prove it. When Perry breaks cover to fend him off, we get this:
Doof-1: Wait a minute, I'm confused. Why does their platypus fight so good?
*Perry rolls his eyes and finally puts on his hat*
The platyposterior as well. Not so good for its intended function, hatching eggs, (at least according to Candace) but great for slapping the crap out of Normbots.
Buford-2 is so good at resisting that he started resisting the Resistance.
Candace-2: Buford - keep resisting!
Just the very fact that the Resistance consists of the Fireside Girls is a hilarious twist. Made even better by their simultaneously girly and badass hideout and Isabella's threatening "Whatcha doin'?"
What about when Doof-1 asked Candace to unlock his chain while they were dangling over lava?
Candace: Are you even paying attention?!
Doof-1: (realizes where he is) Oh, right. It can wait.
Also his realization that the self destruct button on the portal generator is unnecessary, and the fact that he later lapses and includes one when he rebuilds the portal generator.
Existentialist Trading Cards, for all you philosophers out there.
"I'll trade you two Satres for a Nietzsche!"
And Baljeet's reaction when the trade was complete, Genius Bonus or not:
Phineas and Ferb using Doof as a bridge between planets in a different dimension, followed by a comet(?) burning him.
On his butt, no less.
You can always get a good laugh out of a grown man wearing an eyepatch and an evil black labcoat hugging a toy train.
Perry entering Dr D's place: he bursts in, all action as usual...then sees the boys. Cue slow-motion fall to the ground and Oh Crap face.
Some of the dimensions that they pass through on the long way home feature funny shout outs to recurring characters including the Psychedelic Zebra that always calls Candace Kevin (they even seem to recognize each other), the giant green alien from "She's The Mayor", a Q*Bert dimension, and a dimension full of Giant Floating Baby Heads.
Even better, when Candace sees the Zebra, she quickly pretends she doesn't know him while he grins. And the newspaper the Zebra's reading reads 'Kevin Wins Election'
And the newspaper's image is a silhouette of Candace behind a podium.
Made hilarious by the note on the packet 'Even if you win by forfeit'.
Some of the very random explanations for the gadgets Perry's given.
Platyborg getting a roast chicken stuck to the back of his stinger tail and then his head, and Perry's reaction.
May or may not be intentional, but in the online game "Robot Riot," Phineas' reaction upon finding out that Perry is a secret agent is completely opposite of his reaction in the movie, presumably to simplify the plot.
Game!Phineas: "Perry is a secret agent? Cool!"
Stacy talking to the "mysterious force," making a shrine for it, asking it to bring Candace back...and then when Candace does reappear, Stacy follows-up by asking for a car, too.
"A unicorn Stacy, a unicorn! (in childlike voice) Hi, I'm six!". Because it was quite a Take That against the non-periphery demographic and she was so cute when she did it.
"Perry, no! We do not bite the elderly!"
Naturally, the deleted scenes contain all sorts of gold, but the one that stood out the most was this:
News Anchor: Good morning, Danville! Here's our top story...Well, what appeared to some to be a giant invasion of killer robots from another dimension actually turned out to be...a weather balloon! And now, here's Kip Morris with the weather.
The movie tie-in magazine includes a comic on how Doof-2 turned his Perry into the Platyborg, as well as the Amusing Injuries that occured while trying to program him, the first of which being the scar over Doof-2's eyepatch. ("Now I look like a fool!" "I think it looks trendy!" "Quiet, Normbot!") After several weeks of this, Doof-2 finally succeeds in getting Perry-2 to obey his commands without causing hilarious accidents. He sends Perry-2 and his robot army out to conquer the Tri-State Area, expecting all to know his name. The newspaper headline next day reads "Platypus conquers Tri-State Area"
Doof-2: You have got to be kidding me! Curse you, Perry the Platyborg.
"Everything's Better With Perry" has hilarious lyrics of the Mundane Made Awesome variety. It's also quite amusing the way Phineas and Ferb have their whole room programmed to interact with Perry as they start their day. And then there's Ferb singing backup.
In the same vein, "Summer (Where do we begin?)" features a clip where Ferb is holding a hose and accidentally sprays Phineas with it as the latter approaches. So he holds the hose up and sprays himself in the face, too. Infallible logic.
Phineas-2: Mom says that talking to neighbors is dangerous
Linda-2: (from the basement) It's true!
More funny dialog:
Candace: You guys are so...Wait, why are there four of you? Are we inside the mysterious force? And why is Isabella suddenly fashionable?
Isabella-2: What do you mean, 'suddenly'?
"Seriously, how do I dress in your dimension?"
The ridiculous alarm clock, which wakes Perry so he'll chortle and wake Phineas.
Mrs. Thompson: Oh, just like my neighbor upstairs.
Doofenshmirtz:(excitedly) Yes exactly!
Mrs. Thompson: I'm sorry, he's not home right now, you'll have to come back later.
For a hilarious Freeze-Frame Bonus, on the very brief scene near the end that shows the OWCA building from outside, there is a sign that says: OWCA Headquarters and in smaller print: (Pay no attention to this sign).
All of Doof-2's lines in the accompanying online game are hilarious, as are Baljeet-2 being a Deadpan Snarker and Ferb's reaction to Doof-2's plan to trap the protagonists in a maze filled with Normbots ("Is that the best you could come up with?").
The Norm-Bot with the skull on it's head:
"Get me, I'm a Georgia O' Keefe painting."
In the other dimension, after Platyborg and Perry fight Platyborg Falls of the roof the two were fighting on...and onto a bus. After Phineas, Ferb, and Perry escape, A cab drives up to the building... with Platyborg on the wind shield, crashed,he disembarks, and pays the driver, who asks for a tip, Platyborg then threatens him with a mace.
Also Phineas, Ferb, and Perry's reactions to the Platyborg barely missing being hit by a falling norm bot only to get hit a bus.
During Summer (Where Do We Begin), the boys get carried away and start singing a verse of the show's theme song...but realize quickly they're going too fast for their second dimension counterparts.
The way the second-dimension Doof-themed trains arrive at their destination.
Recording of Doof-2's voice: Nyeeeehhhhhhhrrrrrrrr GET OFF!
In the DS tie-in game (the only version I've played so I'm unsure if it's the same in the other versions), Phineas, Ferb, Perry, Candace, and Doof are travelling through dimensions and they hit a haunted-castle-themed world.
Doofenshmirtz: Monsters?! Hold my hand, Perry the Platypus!
Candace: ...Okay, now that's just ridiculous...
To make things better, once you finish the world you can see that Perry is indeed holding Doof's hand. Almost doubles as a Crowning Moment of Heartwarming when you realise that Perry held Doof's hand, comforting him for the entire journey through the spooky dimension.