The "Too Young" Line
Linda: Candace, seriously, isn't Phineas a little young to be a rollercoaster engineer?
Candace: Well, yes. Yes he is.

Ferb: Or you could say "seize the day" was English for "carpe diem."
Phineas: Yes. Yes you could.

Ferb's Line
Ferb: Hmm, what assurance would we had that everyone else will also break into the song and do the same thing?

Phineas: I don't know. I think they probably will.
Ferb: Fair enough, I'm in.

Isabella: That was great, Phineas! So, what are you gonna do tomorrow?

Phineas: Well, you know what they say- carpe diem.
Isabella: Excuse me?
Phineas: Carpe diem. It's Latin for "seize the day."
Ferb: Or you could say "seize the day" was English for "carpe diem."
Phineas: Yes. Yes you could.

Whatcha doin'?
Phineas: Hey Isabella.
Isabella: Whatcha doin'?
Phineas: Building a roller-coaster.

Perry crashed through the roof and landed right inside a glass cage. Before he could do anything, the top of the cage closed, and Perry scowled. Doofenshmirtz had an uncanny ability to predict the exact place where Perry was going to break in. It was his one real skill.

He could see Doofenshmirtz on the other side of the room, adjusting a big Inator. After a few seconds, Doofenshmirtz finished what he was doing and turned around. "Ah, Perry the Platypus. How good of you to... Drop in!" He laughed manically for a second, then got down to business. "You know, I've told you a lot of backstories since we became nemesises." He paused. "N... Nemeses? Whatever. And it got me to thinking. My childhood was terrible! I mean, I knew it was bad, but I never realised..."

He cleared his throat and indicated today's Inator. "That's why I built the Time-Portal-Inator!"

So he just wanted to improve his childhood. That wasn't evil in of itself, but Perry had a feeling that it was a bad idea to mess with your personal timeline. He just couldn't remember why. Maybe Doofenshmirtz would explain it to him. He didn't seem like the type to care about the...

Though Perry and Doofenshmirtz regard each other as a nemesis, their relationship is more along the basis of "friendly enemy".
Doofenshmirtz habitually explains his plans before carrying them out and Perry always stops to listen.
Doofenshmirtz always anticipates Perry the Platypus's entrance and even begins to become anxious if he doesn't show up. He also tends to let Perry into his own home or lair should he discover Perry's presence before Perry has the chance to break himself in. In fact, the two of them are so used to one another being in each others lives that they can't be nemeses with anyone else for more than a day or so. They even exchanged genuine Christmas presents. At one point when Perry the Platypus refused to foil his plans, he followed constantly telling him to thwart him.Perry always saves Doofenshmirtz from death, when Dr. D created his own aluminum siding business, Perry rescues him when it is on the brink of explosion.