Badass Decay: In Ancient History, Ghost Tucker isn't as powerful as Tucker was when he had ghost powers. Justified as Danny believes that when he separated the ghost from Tucker and broke Desiree's spell, it De Powered Ghost Tucker.
Broken Base: Despite the series' popularity, many fans are divided on the concept of Sam having ghost powers.
Development Hell: More than once, the author has had a frustrating time getting a story out.
Growing the Beard: Following A Family Thing, the series seems to be coming into its own. Even Word of God has said that it was the story where the series would start really forming.
Hilarious in Hindsight: To those who have read "A Family Thing" and seen the T.U.F.F. Puppy episode "Sweet Revenge", you may notice that one of Butch Hartman's writers thinks a lot like the author or one of his assistants.
What She Wants revealed that all of the teens in Sidney's ghost Casper High will be there forever. Sidney only gets out thanks to Desiree hearing him while on a wish-granting spree, allowing him to graduate. Now think of other students who are probably miserable like Sidney was and can't graduate...
Word of God likes to wonder if they are real ghost students or rather just extensions of Poindexter, much like the band Ember had in her first appearance.
Vlad's Mind-Control Device: Some little tiny ring shaped device can be stuck behind your ear, where no one will see it. It will completely override your thoughts and turn you into a puppet. Then a ghost like Vlad can turn intangible, sneak up behind you, and put it there.
Nocturnes's plan for Danny and Sam in Hearts and Minds. Trapping them in a dream where they had no memory of each other was bad enough, but he actually attempted to steal all their dream energy and leave them trapped in a Deep Sleep.
Danny's alternate ghost mode. Not only does it cause Danny to slowly become feral, but after using it for too long, the ecto energy will build up to the point where his body will burn out.
Sleeper Hit: When Facing the Future first came out, everybody thought Aaron12 was just another small-time fanfic writer who had a clever premise. Now, he's become one of the most popular DP fanfic writers and fanartists out there, with his popularity growing with each story and pic he publishes.
Squick: In-Universe example. Tucker and Valerie were visibly creeped out seeing Danny and Sam making out while Sam was dressed as Danny. Of course, many viewers have this same reaction upon seeing the pic the author drew depicting the scene.