Big-Lipped Alligator Moment: In "Blackwatch Plaid", after a short series of security camera footage, the episode suddenly transitions into a montage of a live-action Birdman doing completely random things. This has absolutely no bearing on the rest of the episode and is never brought up again.
"Whoooooo... is the man in the suuuuuit?" The song turned out to be so awesome that it spawned a television show. Supposedly, the only reason the show exists is because the creator improvised the theme song at some Williams Street party as a joke. They really liked it.
The musical interlude in "Blackwatch Plaid".
Crosses the Line Twice: The entire "Deadomutt" two-parter from season one, which involves Birdman murdering a dog out of jealousy, going to trial for murder, being found Not Guilty, having that verdict overruled and sent to prison on death row, spending five years in jail, getting married to a gorilla, and then finally being sent to the electric chair...at which point it is revealed that the whole ordeal was actually a big prank thrown for Birdman's 40th birthday (a Call-Back to Birdman stating he is thirty-six in the first part), and that the dog he apparently killed is actually fine. Birdman fails to see the funny side, especially when it's revealed the marriage is totally legit.
In "Guitar Control", which aired around election season of 2004, Phil runs for President of the United States. His voice actor, Stephen Colbert, would go on to do the same by the time the next election rolled around.
Scapegoat Creator: Stephen Colbert; after retooling the show to focus on his characters and their exploits, the show fell apart when he bailed upon it and was quickly cancelled. He also held the blame for the failure of the Harvey Birdman video game, which used the popular Phoenix Wright game engine. Most reviews of the game pretty much focused exclusively on his refusal to voice his characters and the resulting piss-poor replacement voices that Capcom had to scramble to get to replace him.
Squick: Phil Ken Sebben lusting after Birdgirl. He is repeatedly told the truth but doesn't believe it. Near the end of the episode where he and Birdgirl are to be married he looks out over the crowd and decides "...there... might... have... been... someone... else... (he)... was... meant... to... be... with". Birdgirl's aunt Phyllis, Phil's sister!
Not to mention how Aunt Phyllis looks just like Phil with a blonde wig and very large boobs in a dress. Yes, the eyepatch and mustache too.
When he finally does understand who Birdgirl is (in the last episode) he is utterly disgusted and disappointed in her for trying to get into his pants. Especially since he's helpless, with the one eye. ...in his pants.
The Scrappy: Referenced with regard to the Trope Namer. When Scrappy dies, everyone laughs. Especially his "Uncle Scooby."