While other characters simply call him Perry, Dr. Doofenshmirtz always refers to Perry by his full name (Perry the Platypus). He doesn't abbreviate the names of his other nemeses either (Peter the Panda, Planty the Potted Plant, et cetera).
There's a theory that Doofenshmirtz is the biological father of Candace and Phineas, because both Phineas and Doof has triangular heads, both Candace and Doof have long necks, and there is an episode in which Linda and Doof are seen on a date. If Doof is Candace and Phineas's biological father, then it would be assumed that Doof had an extramarital affair with Linda because Candace and Vanessa are the same age, and Vanessa remembers when her mother and father were married before they divorced.
Phineas and Ferb Get Busted, Phineas and Ferb's Quantum Boogaloo, Wizard of Odd and Ferb TV are the only 4 times there has just been a single plot line revolving around Phineas, Candace and Ferb. Additionally, Road to Danville, This is Your Backstory, Sidetracked and Live and Let Drive are the only 4 times there has just been a single plot line revolving around Perry and Dr. Doofenshmirtz.
According to Dan Povenmire and Jeff "Swampy" Marsh, Phineas and Ferb and their friends are supposed to be 8 years old. This also aligns with the episode Act Your Age when the kids are choosing where to go to college, which usually takes place between ages 17 and 19.
The trivia items below may give away important plot points.
In the episode Rollercoaster: The Musical, when Candace is showing her mom the rollercoaster, you can see the two Candaces from the future hiding behind a car. Which means, when the future Candace went back to the past, she went back to the day of the roller coaster (the Musical), not the first day of summer.
In the series finale, while the kids are riding Phineas and Ferb's grand finale ride, for a brief moment, they are transformed into versions of themselves that are animated in the style of a traditional Disney character. Then immediately afterwards into photo realistic versions of the actors voicing them. That is, with the exception of Buford, who is not effected at all, and then transformed into an octopus, before all of them are returned to normal.
In the series finale, Baljeet is looking at a list of possible coordinates on a GPS device. Although the Northern coordinates are in the correct format, the Western hours are missing. If 00 are substituted for the missing numbers, the majority of the coordinates on the list, would be in Northern Africa.
Phineas and Ferb are stepbrothers. Yet, in an episode, they are trying to help their parents celebrate an anniversary by getting Love Händel back together. Considering that Love Händel is meant to be an "80s" band from before the birth of Phineas, Ferb, or Candace, leaves me wondering what the filler should be in this plot hole.