Banned Episode: A rather tragic example of one too — "New Partners on the Block" was banned following an Oklahoma bombing in 1995, and was never allowed again, not even in the six years preceding 9/11. This episode bridges the gap between the Piquel and Miranda episodes too, leaving a rather notable Plot Hole in its place too. On the lesser known side of things, "Fall Apart Bomb Squad" was also banned due to portraying similar bomb terrorist acts, though that one isn't quite as important due to being a typical episode of the show.
Keep Circulating the Tapes: Only six total episodes were released on VHS (and all were Lucky episodes); the rest are unaccounted for. And good luck trying to find the episode that was banned from Toon Disney due to the Oklahoma bombing (and later 9/11), because that hasn't been seen for even longer than the rest of the show.
Word of God: Greg Weisman, co-creator of Gargoyles, helped developed Bonkers and has, apparently, for years been trying to get it through fans' heads that Bonkers was not conceived as a replacement for a Roger Rabbit cartoon that never came to be. There were never any plans for a Roger Rabbit cartoon, but Weisman and his team certainly would have loved to make one. Instead, they took inspiration from their favorite toon rabbit and channeled it into their original creation. 
Bonkers gets a healthy dose of hatred from the Chip 'n Dale Rescue Rangers fandom. Why? Because Bonkers was the show that bumped Rescue Rangers off the Disney Afternoon lineup, and the fandom has never forgiven the show (or Disney) for it. Rival studio Warner Bros. wasn't too thrilled with the show either; they wanted to use the title "Bonkers" for their own cartoon comedy series, which they eventually named Animaniacs. (The Animaniacs writers rarely passed up a chance to take potshots at Bonkers, like on the Slappy Squirrel cartoon "Slappy Goes Walnuts" where she tries to eat an overly-sugary cereal Skippy likes and concludes that cereal like that is rotting his brain, which is why he likes Bonkers.)