Adaptation Displacement: The series was meant both to avert and to capitalize on this, being based on the earlier 1975 live action Filmation series, but riding on the coat-tails of the wildly popular 1984 Columbia film.
Awesome Art: As always, this show is full of spectacular Filmation background art.
Awesome Music: The theme, which incorporates Bach's "Toccata and Fugue in D Minor," has been considered this.
Ear Worm: The theme song, again. True for the catchy theme of the 1975 series.
Fridge Logic: An episode of the original series has a ghost who's also a werewolf trying to steal a mystical amulet from the Ghostbusters. The thing is, this amulet can cure him of lycanthropy, which is why he wants it. Which means that for once the ghosts and the busters aren't at cross-purposes: if they'd worked together the werewolf would've gotten his cure, and the Ghostbusters would've learned what the amulet does and how to use it, allowing them to render other werewolves they face powerless.
Harsher in Hindsight: Forrest Tucker who was Jake Kong Sr. died in 1986, the year the animated series came out. It could explain why Pat Fraley was Jake Kong Sr. and Jr. and Peter Cullen was Eddie Spencer Sr. and Jr.
Idiot Plot: Eddie fell prey to a number of these. Numerous episodes suffer from idiot plots, in fact.
Most of the idiot plots could be avoided if anyone involved used their time traveling abilities properly. Admittedly, if taken to the logical limit the series would be an extremely confusing series of temporal plans.
Nightmare Fuel: Ironically, the ghosts and baddies in the show itself weren't really all that scary, likely by design. The area of the HQ where the boys suited up featuring weird abstract demonic artwork however, was.