Actor Allusion: In the final battle, The Beak suit is piloted by Baljeet and Irving, the two characters voiced by actors from 30 Rock.
All There in the Manual: The official movie magazine features a comic showing how Doof 2 transformed Perry 2 into Platyborg, and took over his Tri-State Area, although its canonical status may be in question.
What Could Have Been: "Mysterious Force" was a song originally made for the movie, sung from Candace's point of view. Unfortunately, due to scaling back of the movie, it was scrapped. (It's on the soundtrack if it means anything)
According to Word of God in the orginal ending, it turns out the 1st dimension isn't REALLY the first dimension, but rather another one, different from the regular episodes. So then nothing canonically happened and then they said that universe's Phineas and Isabella would hook it up. They scraped it because they didn't want to piss off the fans.
There's also the fact that the entire crew, and even Dan and Swampy themselves were divided on whether to have this ending or not (Dan was for, Swampy was against). Apparently the amount of fors and againsts was very even, but as stated above, it was eventually scrapped.
Essentially all the deleted scenes. We not only have "Mysterious Force", but also Vanessa (from both dimensions) being in the film, an explanation for why the entire population of Danville didn't need their memories wipednote the robot invasion was passed off as a weather balloon, a longer (and rather heartwarming) version of the scene where Phineas and Ferb's inventions are replicated, and an extended "Robot Riot" (where we see Danny offhandedly tearing out a Normbot's CPU with his bare hand while singing about it). Considering that all the scenes were fully animated and presumably cut only due to time constraints, they are prime extended edition material.