Before going to find Doofenshmirtz-2, Perry pulls off a tag and hands it to Phineas. Said tag turns out to be a locket...which, when opened, fits perfectly into a keyhole that grants the boys access to copies of all their inventions, and a pre-recorded message saying that Perry always trusted the boys and knows they're the only ones who could ever help him if he needed it. Best part? The locket contains three pictures: Perry, Phineas, and Ferb.
The entire cast asking Major Monogram to wipe their memories of their best day ever so they can keep Perry.
Ferb: "We've had a lot of great days, but we only have one Perry."
Perry saving pictures of him, Phineas and Ferb during the adventure, happy and enjoying themselves, and one of their hug at the end. This ending is as sweet as the writers could make it, Fridge Logic as to exactly how Perry got those pictures be damned.
It's implied that the pictures came from the camera that Major Monogram said every member of OWAC comes with so the organization can reconstruct their enemy's weapons to determine the measure of the enemy's intelligence. Perry also used the camera for unathorized purposes by taking pictures of Phineas and Ferb's inventions so they can be reinvented in case of a dire emergency (see the example above).
Thats not the fridge logic in that troper was talking about. Its the fact that Perry had photos of them smiling at the camera and having fun, when the boys were clearly mad at Perry at that point and simply would not have posed for those earlier photos.
Kind of a small one, but Doofenshmirtz, when finally meeting Phineas and Ferb, is perfectly polite and affable towards them after their offer to help him fix his inator, even offering them part of his buffet.
It's kind of adorable seeing Doofenshmirtz lifting Phineas up so he can install the last part of the Other Dimension-inator, especially when you consider that Doof was perfectly capable of doing that much himself, but probably noticed how much Phineas wanted to do it. Almost enough to make you think that Phineas and Ferb might even be able to dissuade Doofenshmirtz from the path of evil, given the opportunity to spend a little more time with him.
Doofenshmirtz also lets Doof-2 know that the boys are with him, and is appaled when Doof-2 orders Platyborg to attack them. He basically treats the boys like a couple of new best friends before he even meets his counterpart.
A bit of Fridge Heartwarming: when Doof introduces himself, he says "My friends call me..." He's unable to finish that sentence. Soon afterward, Phineas calls him "Dr. D". Now he can. Or at least he could've
Taking this a step further, the song "Missing My Nemesis" in "It's About Time", sung from Perry's point of view, also addresses Doof as Dr. D. showing that Perry does see Doofenshmirtz as a friend.
Also, Doof's first meeting with his counterpart and the song they share. When you take into consideration how lonely Doof usually is and how even with his relationships with Perry and Vanessa, he's never had someone who understands him completely until now, it's kinda sweet. Of course 2nd Dimension Doof then turns out to bea total psychopath...
After the climactic battle, the alternate Phineas and Ferb reunite with Platyborg, and are very happy to see him. They don't even care that he's half-machine now, they're just happy he's home (and think he's a bit cooler now that he's part-machine anyway). Then Platyborg and Perry share a brief smile and salute as they leave. Bonus points because in an earlier scene, the alternate Phineas and Ferb were worried and missed their Perry.
It would be surprising if you didn't see it coming a mile away, but it's notable that, after 2nd Dimension Doof has had Platyborg attack Perry (in pet mode) to make him reveal himself as a secret agentnote which is rather adorable in and of itself, since the boys immediately rush over and fuss over him, he alters the plan and has the robot attack the boys instead. Perry's reaction is immediate.
When Phineas is terribly distressed and repeating to himself "He's a secret agent! He's a secret agent!", Ferb silently tells Phineas, by touching him on the shoulder, that he needs to calm down and focus on the task at hand. For some reason, it's just a sweet brotherly moment of Ferb's part.
Speaking of sweet brotherly moments, Ferb gets a second towards the end of the movie. Blink and you might miss it, but when Doof-2 is about to pound them with his ginormous Final Boss, Ferb is standing in front of Phineas and Perry, ready to take the bot's blow first.
When Phineas and Ferb learn that Perry had been keeping duplicates of their inventions in case he ever needed their help, and Phineas realizes that Perry trusted them.
Not to mention Perry's look of pure joy upon seeing that Phineas and Ferb got his message and have indeed come to help out.
Isabella and Phineas finally kissing!
Made even better (or worse) by Phineas' smile and how he suddenly begs Major Monogram to wait before hitting them with the Amnesiainator.
It may just be me, but Stacy building a shrine to the "Mysterious Force" that she had previously not believed in just in an attempt to get her best friend back, is kinda sweet.
It's not just you. The sheer elaborateness of the shrine she eventually produces is CMOH in and of itself, and she gets extra points for including the boys in her request.
Throughout the movie, Candace-2's devotion to protecting her brothers puts all questions about how much Candace-1 loves her brothers to rest. Especially when Candace-1 says that she does her busting to protect the boys too. Unlikely that it's the only reason, or even true, but still nice.
That's right, we're bros, we're brothers, different father and mother
So don't you diss or slam or sleight us, we look after one another.
In context, it's even better. It's heartwarming enough when you apply it to Phineas and Ferb, but it turns out to be about Phineas, Ferb and Perry. So in a way, Perry is a brother too.
When Phineas-1 and Ferb-1 first meet Phineas-2 and Ferb-2, Phineas-2 is overjoyed to see Perry. He thinks it's their Perry, who's been missing for a long time. When Phineas-1 tells him it's actually Perry from their universe, Phineas-2 asks if he can hold him for a little longer anyway. Both Ferbs start tearing up.
Phineas-2 and Ferb-2 helping to bust Candace-2 out of prison and the hug the three of them share with Candace-2 saying she's proud of them.
Some Fridge Heartwarming for anyone who felt sorry for Norm in the episode "A Real Boy"—when the Norm-Bots start getting destroyed, Doofenshmirtz-2 wails, "My babies!" Of course, it gets cancelled out big-time when Doof-2 turns good and hits the self-destruct remote to clean up the mess.
A cross between Heartwarming and Awesome, but Phineas getting Alternate! Phineas and Ferb to sing "Summer (Where Do We Begin)?" with him.
It's also a good indication of just how timid the Alt. boys were in the beginning— when they got Alt. Ferb to sing his line he didn't look comfortable with it in the slightest. You could go so far as to say that he looked harassed. The sheer amount of progress they made over the course of the movie fits squarely into Crowning Moment of Awesome as well as heartwarming.
Phineas sings that sitting with his brother under the shade of a big tree is what summer means to him. For all of their ambitious projects and outrageous adventures, Phineas could be happy doing nothing all day, as long as he was with Ferb.
Phineas's speech to Perry at the end of the movie about how he now and always will consider Perry to be a great pet and a great friend.
The deleted scenes have a longer version of the scene where Phineas and Ferb discover their scanned inventions. At the end of the scene, Phineas is delighted to realize that Perry saw all their activities after all!
The end of the battle, where the now-good Alternate Doofenshmirtz, after proving to be more competent than our Doofenshmirtz, had his own self-destruct button for the Normbots on a remote in his pocket. It's charming, in a Narmy sense.
I CANNOT believe I am the first one to notice this. When Phineas-1 and Ferb-1 fail to recieve any help from Phineas-2 and Ferb-2, Phineas-1 suggests they go seek Isabella-2. In their dimension, Isabella-1 isn't as smart as Phineas-1 and Ferb-1. Baljeet-1 is. This shows that if there is any one of his friends Phineas-1 trusts the most, It is Isabella.
YMMV Isabella seems quite smart. This rather means that Phineas trusts Isabella's problem solving more than Baljeet's.
Isabella telling Ferb "We'll handle it down here! Go help Phineas!" If she was only worried about Phineas, she could have just gone herself to help him, Action Girl that she is. But she was aware enough of Ferb's feelings to know where he really wanted to be, and clear his way to get back to his brother. Despite the fact that her crush keeps her focused on Phineas most of the time, Isabella is still Ferb's friend, and a good one at that.