Crossdressing Voices: It was initially played straight for the nerd Mikey, who was voiced by Colleen O'Shaughnessey in his early, minor appearances. Subverted later on when he's voiced by Dee Bradley Baker.
Whatever the reason, Steve Marmel was no longer involved with the series after season 2. Whatever the plans he had to use for season 3 were never used or revealed.
A positive example: it was the higher ups who suggested that Hartman give Danny a logo.
According to Hartman, the primary reason for the show's cancellation was that the studio executive who was championing the series left Nickelodeon and the network wanted to put more focus on Avatar: The Last Airbender.
A good example of this particular flipflop is Dora the Dragon Ghost, who is heavily implied to have once lived in her first initial appearance, but doesn't seem to have ever lived as a human in her second appearance.
Another example of a flipflop is Ember McLain. Her actions, language and attitude suggest she's a teenager with a desire to rebel against adults, which might be the reason she was getting constant shipping with Danny from fans. However, the idea of them having this kind of "relationship" didn't occur when admins on Hartman's forums stated she was much older, around her early 20's... which technically makes her an adult. Suddenly she's Skulker's girlfriend... and Skulker himself is an adult.
Lying Creator: Butch Hartman has said the ghosts are not meant to be spirits of the dead, despite many of the ghosts in the show are shown to once have been alive (Pointdexter, Desiree, the Dairy King, the Lunch Lady, Ember). See Flip-Flop of God.
A Part-Time Hero named Fenton. Also, Tucker shares the same last name with Richie Foley from Static Shock who is also a nerdish technologically obsessed side kick who does scheduling for the protagonist.
Non-Singing Voice: Weirdly enough, Ember. She's voiced by Tara Strong, who has a great singing voice, but her singing voice is provided by Robyn Kirmssé instead for some reason.
"The Fenton Menace" and "Identity Crisis" aired after "The Ultimate Enemy" but were set beforehand.
Despite being set afterwards, "Double Cross My Heart" and "Kindred Spirts" aired before "Reality Trip".
In addition, "Urban Jungle" was the first episode of the third season to premiere, even though it was number six. The Season 3 premiere didn't even air in the U.S until after the following seven. Honestly, Nick didn't handle new episodes very well.
The DVD sets place the episodes in production order. This isn't really a problem for Seasons 1 & 3 (in the latter's case, it even puts "Urban Jungle" in it's intended spot), but it is for Season 2 as certain episodes that took place earlier that season were produced later such as "Memory Blanked" which was the season premiere (and the episode where Danny gets his logo) but the sixth episode produced that season.
Danny was supposed to be a teenaged Ghostbuster on a motorcycle with a pet owl and a psychic link to Sam. Then the idea was tweaked into what it is now.
The motorcycle ghost idea eventually became Johnny 13.
The pet owl was going to be named Spooky, and would help Danny find ghosts. But Harry Potter (particularly the films) was getting big at the time and Harry already had a pet owl, so the idea was scrapped.
Sam and Danny were originally meant to share a psychic connection before Butch Hartman decided against it, saying only Danny should have the special powers.
Butch Hartman originally wanted Danny to be voiced by an actual 14-year-old but couldn't find anybody who sounded "heroic" enough.
This could apply to the entire third season, as Steve Marmel allegedly wanted to get Darker and Edgier, following along the lines of "The Ultimate Enemy". There was even a fan project on imagining what it would be like, only it never got off the ground because they couldn't get details from Mr. Marmel. Marmel won't comment on what Season 3 was going to be about or why he was let go, mostly out of respect for his former partner Hartman.
According to Word of God, Danielle was meant to be revealed to the Fenton family and become Danny's little sister. Yet another plotline that was abandoned when the series was abruptly canceled.
The series was originally meant to end with a final battle between Danny and Dark Danny. One could argue it would have made a greater series finale than Phantom Planet.
According to writer Steve Marmel, an original Running Gag would be that Vlad's manor would blow up every time.
The show had a vastly different intro, being sung rather than rapped. The rhythm was the same but the lyrics were not. You can watch that original intro here. There's also a third version of the intro according to composer Guy Moon, one that has yet to be seen by the public.
Some of Danny's original first names include Kenny and Davie.
A planned toyline was cancelled due to the show's sudden cancellation.
Post-series, Hartman retconned ghosts into a ghost-like species that takes the appearance of deceased people. This is despite many characters being shown to be literal ghosts.
Word of God is that Ember is in her twenties. She is called a "teenager" in her debut episode.
Ember's official backstory doesn't match the lyrics to "Remember". Ember apparently died the same night she was spurned by her date, however the song has the lyrics "Three weeks you didn't call". The official backstory also doesn't explain why fire is so important to Ember if it was just a freak accident.
The name "Vlad Plasmius" was claimed by Marmel to be written on a brick he bought.
Tucker Foley was named after Chris Tucker and Eddie Murphy's character Axel Foley from Beverly Hill Cops. Jazz was named after a character from the Next Men series. Vlad is derived from Vlad Dracula III, the original inspiration for Dracula.
For that matter, Vlad was originally intended to be a vampire, hence why his ghostly form heavily resembles one.
Also, hence the name "Plasmius"—from "plasma," or blood.
Danny Phantom's eyebrows were at one time (in production) white like his hair, but they were changed back to black—they made him look too old.
Look at Sam's room right after the theme song in "Control Freaks." Sam has a (musical) keyboard lying on her floor. Perhaps she plays!
Also, there's a red version of Ember's guitar in Jazz's room in "Fanning the Flames".
In a first season episode, where Tucker is editing his grades, the only ones he has A's in are Computers and ...Sewing.
According to one of the admins on Butch Hartman's forums (before the site eventually ended), Hartman stated not everyone can become a half ghost the same way Danny and Vlad did. Meaning if it were Sam or Tucker who entered the portal, it would have more likely killed them than turn them half ghost.
The show's/Danny's constantly noted resemblance to Spider-Man is hardly surprising once you learn one of the writers, Marty Isenberg, wrote 6 episodes of Spider-Man: The Animated Series.
Butch Hartman was heavily inspired by Jonny Quest in making the show.
Amity Park was named after The Amityville Horror (1979) as well as Amity Island because the show's creators wanted a scary-sounding name for the town, as the show revolved around ghosts and/or monsters.