In the song "With a Dart," Dr. Doofenshmirtz says he'll go unconscious in 17 seconds, and, per his statement, it really does take 17 seconds for him to faint.
In "Bad Hair Day," Jeremy's mom reads the instructions for the tranquilizer dart gun. She reads "there are many like it but this one is yours" which is a reference to the movie "Full Metal Jacket" when the marines are in boot camp.
In "Meatloaf Surprise" the band Tiny Cowboy, Adrian and Nigel, are voiced by Davy Jones and Peter Noone. Both were lead singers in popular bands from the 1960's, The Monkees and Herman's Hermits, respectively.