Pokémon: Indigo League
Electric Soldier Porygon
The 38th episode in the original Pokémon series was banned from broadcasting in Japan, and subsequently prevented from ever airing in any other country. There is apparently a scene where Pikachu thunderbolts some missiles, resulting in some very intense flashing blue and red lights. The episode caused headaches, seizures, nausea, and numerous other ailments. According to the voice of Meowth in the American dubbed version, there was an American version created, but after Japan banned the episode, it too was banned.
Warning, the below video is known to cause seizures.
Beauty and the Beach
The 18th episode in the series was removed from airing in the United States initially, and re one time as a "lost episode special". In this episode, a few female characters enter a beauty pageant. James, of Team Rocket, wears a suit with inflatable breasts. James tell Misty maybe someday she will have a chest like his! There is also a scene where an old man is attracted to Misty in her bikini.
The Legend of Dratini
The 35th episode of the series was also banned from playing in the United States. In this episode, a character kind of jokingly aims a gun at Ash. It has been banned in every country but Japan.
Tentacool and Tentacruel
After 9/11 a couple different TV series had to change their rotations. In this episode, there is a character that uses military weapons as Tentacruel attacks a city. There's a shot of Tentracruel attacking a building, which is probably the real reason this episode was banned, yet there is a clip of this episode in the opening that still remains. This episode was banned again after Hurricane Katrina.
The Tower of Terror
This one just seem silly, but I guess they all do. The 23rd episode in the series was temporarily removed around 9/11 because it features some ghost Pokemon scaring people in a tower...
Talespin
The final episode, number 65, of Talespin was for having terrorists in it. The main character, Baloo, is tasked with delivery a package to some government official, but the package is actually a bomb.
I tried to upload the episode, but it was removed before I could even copy and paste the link here. Disney doesn't want it going out.
Gargoyles
In the eighth episodes of Gargoyles, one of the Gargoyles, Broadway, is playing around with their cop buddy's (Elisa) gun and accidentally shoots her.