The fact that it does not end with mourning for those events, but Perry happily holds on to the memory of the best day ever.
Phineas and Ferb meet their counterparts, and the alternate Phineas sees Perry and immediately hugs him, thinking he's their Perry, finally come home. When Phineas tells him that it's the wrong Perry...
Phineas-2: Wait...can I hold him a little longer?
Even Ferb (both of them, in fact) got teary-eyed at that part.
Made all the more poignant when you remember how heartbroken our Phineas and Ferb were when Perry vanished for one day. The alternate Phineas and Ferb have been without him for months, at least.
"I Walk Away". That is all.
"I thought you couldn't spell 'platypus' without 'us'." Though, after a pause, Ferb makes a reply that makes this more of a funny moment.
The final scene mostly heartwarming, but the last photograph◊, with Phineas and Perry sadly hugging... *sniff*
The scene where all of Phineas and Ferb's friends and inventions arrive one by one in all their glory, fully ready for battle. It's not a scene where you'll shed tears of sadness, but some may shed tears of joy at the return of all the past inventions and the realization that something really, really awesome is about to happen (which it does).
Stacy begging the "Mysterious Force" to get her best friend back. She sounded like she was close to crying. This troper can assume that after Candace came back (and she begged for a car), Stacy gave her a tight hug in a missed moment of heartwarming.
Is this troper the only one who thought the scene where Phineas was shouting "Wait! Wait! Wait!" like he wanted to say something to Isabella really sad? He never got the chance to, and he forgets the kiss.
When the main characters are all dangling off the side of the goozim cage, Perry is clearly in great anguish, knowing that if he fails, he will doom not only himself but also the four individuals who he cares for the most.