Taken from “Could Dr. Doofenshmirtz be Phineas and Candace’s Biological Father?” from Heinz84’s Phineas and Ferb Fanon Wiki Blog.
I personnally believe that this is a strong possibility. After all,
Doofenshmirtz and Phineas have so much in common. They both have a triangular shaped head, have a similar palm-tree hair style, and They both like to invent all sorts of devices and contraptions to solve their problems. And if this case is true, then when the two finally meet in the series, it could be one of those “I am your father!” moments.
Also, Candace and Vanessa have a lot in common, as they both try hard to bust their schemers, and both have a similar attitude, as seen in their song, “Busted”, or was it “Bust em”? so they could be half-sisters, and their evil, “busting” gene could come from Doofenshmirtz.
So I think it is very possible that Dr. Doofenshmirtz could be Phineas and Candace’s real father. What do the rest of you think?