A number of third-party manufacturers have even begun making Warhammer-compatible "Space Dwarfs," such as the Forge Fathers by Mantic, and numerous fan-made codexes exist to make Squats compatible with the current version of the game. Games Workshop does not allow third-party figurines and fan-made codexes in official events, however they do allow vintage Squat figurines to be used as long as they are drafted and played under different, "acceptable" army's official rules (typically making Squat units into a reskin for the Imperials).
Warhammer Fantasy also has the Firmir, a race of Cyclopean monsters that were essentially entirely excised from the fluff and had their army discontinued. Much of this might have to do with the questionable way they reproduce. Recently they've gotten little minor references in the rulebook, a summoned monster in Storm of Magic and a few Forge World models, but a new book is highly unlikely. Chaos Dwarves also seemed to be going that way, but they recently started get large amounts of reference in the fluff, mostly due to their proximity to the Ogre Kingdoms and their popularity with older players. Every time there's even a hint of something new coming, everyone will declare it's the Chaos Dwarves.
Later editions of Vampire: The Masquerade did their damnedest to sweep everything from the Dirty Secrets of the Black Hand supplement under the carpet.
World of Darkness: Gypsies was embarrassing for its racist stereotypes. Later sourcebooks that dealt with the Roma pointed out the book's stereotypes, and explored how actual Roma would likely deal with the supernatural.
Gary Gygax said that he regretted a number of rules that he felt pressured to put in various versions of Dungeons & Dragons, singling out psionics, the monk class and weapon speeds and effects versus armor as egregious examples.
The sexism of 1st Edition AD&D (most infamously memetic being the "women suffer a -2 penalty to Strength" rule) is likewise something which later editions' designers would very much like everyone to forget.
Urza's Saga block, which was massively overpowered and created the most unfun standard environment in history, according to Mark Rosewater the only block where "The entire team got called into the boss's office and got yelled at." To a lesser extent, any other overly format-dominating cards/archetypes.
On the other end of the spectrum there are Fallen Empires, The Dark, and especially Homelands, widely considered the weakest sets. The game, at the time, had been having problems with overly powerful cards, and had corrected too far in the opposite direction. Fallen Empires also has the distinction of being overprinted as well, making cards and packs next to worthless.
Magic originally was supposed to be played for "ante": Each player, after shuffling but before drawing their hand, took the top card of their deck and set it aside; the winner of the game got both cards. This made the game a target of anti-gambling laws, and Wizards would eventually do away with the ante rule (and ban cards that dealt with ante). Wizards tries very hard to keep that link between its game and gambling under the table (although it could be theorized that the game's strategic elements make it the perfect "gateway game" to poker, as evidenced by David Williams et al.)
Every trading card game gets hit with this. You have this one card that quickly becomes exploited to death by the hardcore players. As a result, the card deemed responsible is placed onto the banlist, never to return to normal play.
Exalted has the much-reviled Scroll of the Monk, for writer Dean Shomshak. The first thing he did upon becoming an Ink Monkey was apologize for writing it.
A number of the current writers, notably Holden Shearer and John Mørke, have stated that in hindsight, they really wish they hadn't done about half the things that went into late second edition, because they feel the focus on high-Essence play and the spectacular and cosmic stuff papered over the pulp fantasy the game was actually supposed to be about.