When Batman is going through the filing cabinet, searching for Bullock's file, he passes a file for J. Barr (James O'Barr), who is the creator of "The Crow" comic book series. He also passes an "N. Bate" file, which could be a reference to Norman Bates from Psycho (1960).
The first time Waylon Jones/Killer Croc makes his appearance.
In the original script, written by Michael Reaves, the ending shows Killer Croc escape to a Seaworld park where he gets knocked into a pool of electric eels. Frank Paur rewrote the ending and it's his ending that is shown.
Spider Conway may refer to Killer Croc's co-creator, writer Gerry Conway (who also wrote Spider-Man for a time, perhaps explaining the animated character's first name)
Originally Killer Croc's first story was going to be his origin story which would have been greatly different from his origin in the comics. He would have been an animal trader who was bitten by a lizard, giving him a disease that mutates him into Killer Croc, who then plans to create an army of reptiles in the sewers to terrorize Gotham. Obviously this story was scrapped because it was deemed too far-fetched.