As a rule, when talking censorship we try not to censor ourselves. Meaning some of this stuff might be NSFW. Mostly on the second page.
1. The whole deal with Jynx
Jynx is not a comfortable subject for a variety of reasons. Though there is some debate among fans (more on that in a sec), most of the conversation revolves around the fact that the first-gen Pokemon bears a downright disturbing resemblance to the horrific, centuries-old "darky" stereotype. Whether you believe that Jynx was designed with blackface in mind is kind of irrelevant -- the fact remains that the ink-black skin combined with the beady eyes and giant lips leaves an unmistakably racist impression. It definitely appears as though Jynx was based on a minstrel stereotype. Hell, this is one of the only Pokemon with a humanoid body; the Pokedex even refers to Jynx as a "Human Shape Pokemon."
Now, no one is saying anyone at Game Freak acted with any malice when creating Jynx, but that doesn't mean it didn't introduce an abominable stereotype to children. Pokemon had been a success for some time before someone got through to Nintendo, however. Starting with Carole B. Weatherford's 2000 article "Politically Correct Pokemon," people began to re-examine Jynx and come away with a mortified cringe on their faces.
Nintendo's response? Keep the Pokemon, but paint it purple.
On one hand, you can almost understand why Nintendo didn't want to outright get rid of Jynx. The name of the game is "Gotta Catch 'Em All," and you can't very well do that with Pokemon #124 locked away in the Vault of Pretending This Never Happened along with Disney's Song of the South. Rather than make its failure to recognize cultural history more obvious with the complete absence of the offending pocket monster, Nintendo altogether minimized Jynx's appearances across the transmedia property. Episodes with Jynx were either either trimmed or outright pulled from circulation.
In the cases where Jynx does appear briefly, the whole "wow yeah, that's actually really racist" situation is remedied by changing Jynx's black skin to something closer to a lavender. This status quo is even extended to rereleases of old material, as evidenced by the N64 version of Pokemon Snap versus the Virtual Console iteration. While it's somewhat comforting that Nintendo (tacitly) admitted that one of its character designs was insensitive, doing a quick palette swap doesn't really change the problem, since Jynx remains just an MS Paint Bucket tool away from from its former stereotypical self.
It's important to note that Nintendo came to this decision of their own accord; though pressured by outside groups who didn't want their kids playing with personified racial slurs, it's not like the government stepped in and decreed that Jynx's skin tone should be changed. You might call this self-censorship, but the way it played out is more of a half-assed apology. Sort of like your racist grandma admitting that "I've never met a Scotsman who didn't smell like a damp sack full of rotten haggis, but I assume some of them are good people."
Even though the "censorship" in this case was justified, that hasn't stopped fans from claiming nothing should have been changed in the first place. Since the controversy, some have taken to the belief that Jynx was based on the "ganguro" fashion trend in 90s Japan.
Forget for a minute that "ganguro" in some circumstances literally translates to "black-face" -- the fact is, the claim doesn't really add up. Pokemon was in development for years and years up to its release in 1996, which doesn't really give Game Freak much time to hone in on a then-obscure fad, much less come up with the justification for creating an entire character out of it.
Others have compared Jynx to that of a viking, what with the armor-like clothes and purple "frostbitten" skin coinciding with being an Ice-type Pokemon. These are all really roundabout ways of attempting to defend a character design that really, seriously looks like blackface. The simplest explanation is that the Japanese developers didn't really understand the implications of what they were doing when creating this Pokemon, and had to backtrack when the franchise became a worldwide phenomenon. Fans defending Jynx's design understandably don't want to believe that such an important part of their childhood could be tainted with racism, so they bend over backwards to weave what are essentially anti-discrimination fan theories.
When it comes down to it, you can compare Jynx's trajectory (and subsequent re-colorization) to a certain Dragon Ball Z character.
If you can describe your character as "Mr. Popo in drag," you might want to re-consider showing this character to anyone on the face of the earth.
2. Americanized anime, and the scourge of 4Kids
We've already blurred the line a little bit, but the term "censorship" doesn't exactly apply to every single change made to source material. Yes, 4Kids is pretty god damned terrible sometimes, but you can't blame anyone for ditching a Pokemon episode where guns are routinely pointed at children. It might play differently in Japan, where firearms aren't as prevalent and could more easily be seen as an exaggerated joke -- but in the land of the Second Amendment, guns are a very real threat that kids should probably not be desensitized to in their favorite cartoons.
In instances like these, context is important. Changing the Pokemon anime to better cater to the country it's airing in isn't necessarily "censorship," but most often just "localization." Even so, some of the changes made to the show as it crossed the Pacific are kind of baffling.
The fix here is subtle, but check out the glass Giovanni is holding -- in the Japanese version, the wine glass has a stem, whereas the USA version has G-man sipping from a tumbler. So whereas originally is almost certainly drinking white wine, the localized version makes that yellowy liquid a little more ambiguous. Does the big bad of the Pokemon universe nurse a glass of apple juice while contemplating world domination? Maybe!
And that's not the only time 4Kids came up with a confusing solution to what might otherwise be a real problem.
In a snowy episode (coincidentally coming right after a since-pulled Jynx episode), Meowth and Team Rocket find themselves fighting for survival in an igloo. All they have for warmth are a few piddly matches, which are lit in vain. Except, in the English dub, these matches magically turn into birthday candles when held in Meowth's hand. You can kind of guess that 4Kids didn't want to show their characters "playing with matches" as to not inspire any budding pyros, but it's not like Team Rocket's evil plan involved church arson. They were just trying to make it in a desperate situation. Instead of showing the direness of the characters' plight, 4Kids reminded everyone they were watching a cartoon by making the talking cat pull a birthday candle out of nowhere. Though relatively harmless, it says a lot that it's insulting even to a seven-year-old.
But if you really want to get into "clueless localization," you have to see the way 4Kids treats food.
Though Pokemon's international appeal is undeniable, ultimately it is still a very Japanese product. Even Kanto, the location of the original games, is based on Japan. So it stands to reason that Japanese traditions and customs would eke into the games and especially the anime, which has to pump out tons of story content each year.
But 4Kids decided against "kindergarten-level anthropology" in favor of a tone more fitting of "condescension bordering on contempt." Instead of just allowing the characters in the show to eat rice balls and give their young audience the very smallest glimmer of real culture in a show about magical monsters, the localization team painted over the distinctly-Asian snack with an American-sized sub sandwich. And when it's too much work to do even that, apparently all you have to do is make the characters refer to the rice balls as "donuts" and hope that no one on the internet notices.
Just because some decisions are indescribably stupid, that doesn't mean censorship/localization doesn't have a place.
Above you can see Lenora, a gym leader from the Black/White era. The big change here likely came from Nintendo themselves, as an updated character design removed the apron wrapped around one of the only major black characters in Pokemon history. The problem was that Nintendo ran into yet another racist snafu, what with Lenora's apron implying the "mammy" housekeeper stereotype. You can't make this shit up.
To make matters worse, that "mammy" impression is backed up by Lenora's characteristics in the original Japanese version of Pokemon B/W. Before coming to the states, her Gym Leader title translated to "Natural Born Mama." Yeah. Not only that, but Japanese players entering Lenora's gym were faced with a series of cooking quizzes, which were changed to general Pokemon trivia for the US release. This isn't a coincidence, and it probably doesn't even qualify as an accident. Someone at Nintendo fucked up, again, pure and simple. "Censorship" in this case is just an oblivious company covering its own ass.
Need another example of those involved in Pokemon having absolutely no concept of what could be considered culturally inappropriate like, anywhere else in the world? Look no further:
On the left, you can see an unedited scene of what appears to be Team Rocket's rousing rendition of "Springtime for Hitler." The scene was changed dramatically when it came overseas, mostly because the US is a politically-correct hellscape that doesn't tolerate challenging ideas like a dozen men giving the Nazi salute in a children's program.
This is all pretty heavy stuff, so how about we finish up the anime examination with something lighter. Like say, inflatable boobs, perhaps?
Maybe the most infamous banned episode of the series (you know, besides the one that gave everyone seizures) is probably the one entitled "Beauty and the Beach." As you can probably guess from that confusing/mesmerizing GIF, it involves James of Team Rocket wielding a pair of adjustable synthetic breasts in order to win a female beauty contest. It seems kind of harmless by today's standards, maybe even progressive depending on how you look at it.
While that episode only aired a handful of times before being taken out of circulation, some of the weirder stuff is still lurking just underneath the English dub.
In the Japanese version of this episode, this kid straight-up stares at Misty's boobs and asks if he can drink from them. This is changed in the US, for obvious reasons, to the child asking whether Misty was a person or a Pokemon. Though it seems extremely skeevy for a show to portray a child wanting to nurse from a preteen, it wasn't originally seen that way. In Japan, the whole "kid who doesn't understand sex" trope is seen as a playful indication of innocence; this same sentiment explains why young Goku can be seen slapping Bulma's vagina in an early Dragon Ball episode.
Whew, that's a lot to take in. And we haven't even talked about the games.