Hilarious in Hindsight: Episode 3 reveals Irving has a crush on Candace. Several months after the fic was thought of, "Moon Farm" aired, in which Irving hits on Candace.
And in the same episode, P&F build a giant ant farm. Guess what the actual show's "Gi-Ants" is about.
An episode was planned called "Mission: Permission" in which Candace throws a party. Later, "Candace Gets Busted" was announced. The kicker? When the author first asked for a possible title to his friends, the first title suggested was "Candace Gets Busted"
A lemur agents shows up in "Where's Perry?", leading to the author to announce he will do an episode explaining that.
In "The Norminator", Stacy finds out that Larry is an agent. Something similar would happen later in the show.
Ho Yay: The fact that Irving watches Phineas and Ferb while they sleep is...interesting, to say the least.
The "Whatever floats your ship" comment as seen on the main page
This, from "Irving's Fan".
Norm: Yay! What do you say, boss? A candlelit dinner with a rooftop view? An exotic gondola ride beneath the stars? A slow dance on the roof under the moonlight?
Doofenshmirtz: Uh, sure, okay. Let's go do that. Though I can't shake the feeling we forgot something. Something important...