According to creator Dan Povenmire on the DVD bonus feature "Original Story Pitch" from The Fast and the Phineas the song was originally going to be done by a classical Disney chorus. He and Jeff "Swampy" Marsh wrote the lyrics, but Disney wanted to make the melody more modern. Dan Povenmire sang an approximation of it on the "Original Story Pitch." Povenmire finally got his classical Disney chorus for the Christmas version of the song.
In reality, summer vacation lasts about 93 days. At San Diego Comic-Con 2013, Dan Povenmire revealed that he wrote 104 because he only expected the show to last 52 episodes, like most Disney Channel shows lasted at the time, and there were two segments per episode, making it 104.
In the episode "Phineas and Ferb's Quantum Boogaloo," Phineas tells Xavier and Fred that Bowling for Soup is "before their time." He also might be referring to the fact that the kids that are watching this show are not familiar with the band, as it is somewhat before this show's time.
"Today is Gonna Be a Great Day" is an extended version of the original theme song, with additional lyrics by Bowling for Soup's Jaret Reddick. He explained to Songfacts that he was brought to the Disney lot and shown the first 13 episodes, which he used to write the full length song. It took him about 20 minutes to write the extra lyrics[1].
The song was nominated in 2008 for an Emmy Award for "Primetime Emmy Award for Outstanding Main Title Theme Music," but lost to "Pirate Master" on CBS.
A form of the song is used in the credits for "Phineas' Birthday Clip-O-Rama!" in which we see clips of Candace yelling "Mom!" the tag-line at the end is "Mom, Phineas and Ferb are digitally tuning my voice!"
Pizzazium Infinionite's atomic number is 104, which may be a reference to there being (at least for Phineas and Ferb) 104 days in summer vacation.
The song was referenced in lots of episodes such as, "Phineas and Ferb's Quantum Boogaloo", "Swiss Family Phineas", "Last Train to Bustville", "Canderemy", et al.
In the title sequence for "Phineas and Ferb: Mission Marvel", Spider-Man takes Candace's place and parodies her line as "Aunt May, Phineas and Ferb are making a crossover!