Phineas digs up a yellow sponge and a pink starfish and then tosses them into the ocean saying "Oh, look, a sponge and a starfish! There's gotta be something we can make outta this! Aw, oh no, that's ridiculous!!". These could be references to SpongeBob and Patrick.
Phineas, Ferb and their friends put up posters and sing a song in hopes that Perry will hear them and come back home. The premise of the search and the song "Perry Come Home" are both quite similar to SpongeBob's efforts to find his pet snail, including the song in the background "Gary Come Home."
Krabby Patty Creature Feature-When everybody in town except Doof turns into Doof zombies,that could be a reference to when everybody in Bikini Bottom except SpongeBob turns intoo Krabby Patty Zombies.-Night of the Living Pharmacists