Fan Nickname: "Clonatello" or "Duplicatello" for Donatello's Evil Twin duplicate he creates in "Donatello's Duplicate".
Executive Meddling: Mona Lisa was originally going to be a female turtle, but Eastman and Laird rejected it, so she was reimagined into some kind of lizard, which is why her head and feet look like the TMNT's. Supposedly they still didn't like her even after these changes, and ordered the makers of the show not to use her again.
Network meddling was also responsible for Shredder and Krang being Put on a Bus and replaced by Dregg during the ninth season. They also forced the show's creators to introduce a "hip" new character, eventually resulting in Carter, who was pretty much a Composite Character of not only Casey Jones and Donatello, but also Keno from the second TMNT movie. After these changes weren't liked by the fans, rather than admit they might have been slightly misguided in these demands, the executives fired head writer David Wise and replaced him with Jeffrey Scott, who had never even watched the series beforenote (and actually ended up persuading Wise to come back as an uncredited co-writer after being unable to get to grips with the characters), speeding TMNT '87 to its demise.
Say what you will about Dregg replacing Shredder and Krang in seasons 9 & 10, you gotta admit having him voiced by Tony Jay makes him a Bad Ass.
Name's the Same: In season eight, there's a villain named Megavolt, who shares the same name as another villainous character named Megavolt.
There's also some Fridge Brilliance in that episode since Megavolt wanted to destroy the D.W.(Dark Water) company out of revenge. D.W. is also the nickname of Darkwing Duck.
Also Baxter Stockman's Mouser robots have the same name as King Koopa (Bowser)'s assistant in Super Mario Bros..
The Other Darrin: Several voice actors would occasionally have replacements during particular episodes:
Shredder was the biggest example, due to James Avery's other work; he was substituted by Dorian Harewood for a lot of the later Season 3 episodes, and them Jim Cummings on and off for the next few seasons. He finally bailed out the show for good at the start of Season 7; Townsend Coleman (the voice of Mikey and the Rat King) voiced him for the rest of that season, and William E. Martin took over the role permanently in Seasons 8-10.
Raphael also had a few different voice actors over the course of the show; Thom Pinto voiced him for a few Season 3 episodes, Hal Rayle filled in for the "Vacation in Europe" episodes, and Michael Gough (no, not that one) replaced Rob Paulsen for the final season.
Donatello and Bebop, who were both usually voiced by Barry Gordon, were also replaced for part of Season 3 (seeing a pattern here?) by Greg Berg.
Vernon Fenwick was voiced by Pat Fraley in Season 1, but for some reason changed to being voiced by Peter Renaday starting with Season 2.
Word of God (David Wise) has admitted April's yellow jumpsuit and minicamcorder outfit was based on Fujiko Mine's outfit from the Japanese anime Lupin the Third. Specifically, her outfit in The Castle of Cagliostro.
Talking to Himself: Constantly, as most of the show's voices were done by a handful of regulars.
What Could Have Been/Missing Episode: There was originally going to be an episode called "Shredder in Love", but it never got past the script stage. Renae Jacobs even recorded lines for it. Little is known about the plot, but rumours state that the love potions from "Green with Jealousy" might have been reused.
Write Who You Know: Zach (the "fifth turtle") was allegedly based on one of the writer's kids.