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.
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.
Also the musical interlude in "Blackwatch Plaid".
Ensemble Darkhorse: Phil Ken Sebben and Reducto. Both voiced by Stephen Colbert. The Bear, as well.
Hilarious in Hindsight: In Guitar Control, which aired around election season 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 holds 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 piss poor replacement voices Capcom had to scramble to get to replace him, in attacking the game
Parodied in an episode when Harvey points out how many cartoons followed the mold of Scooby-Doo, complete with barely altered characters.
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 in to 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."