The mine cars commonly used in the 2nd dimension by The Resistance are the same ones seen being used by the animal agents as Agent Perry descends into his lair at the beginning of the movie. The Resistance Headquarters is Agent Pinky's lair, which is why the giant screen is pink and flowery.
During the song "I Found a New Friend and It's Me", the two Doofenshmirtz's appear as several famous duos including Sherlock Holmes and Dr. Watson, Lewis and Clark, Simon and Garfunkel, and the Lone Ranger and Tonto.
The trivia item below may give away important plot points.
When Phineas says that they could have a lot of fun with Agent P, Major Monogram says "the next 15 minutes should be a real hoot." Some may think he's referring to the length of a normal episode, credits and all; but, with less than five minutes of show remaining, he's actually referring to secret agent policy that calls for Perry to be immediately moved to another home where his agent status is not known. He's saying that Phineas and Ferb have about fifteen minutes with Perry before they never see him again.