We know Nintendo has quite the reputation for being family-friendly, but as the thread title says, it's not always the case. Here's a few examples.

F-Zero, and guns: Believe it or not, guns, and I mean realistic guns, the kind you'd see in the Resident Evil or the Metal Gear Solid games, have made a few appearances in the series. When you beat a cup in F-Zero X as Blood Falcon (who drives the Blood Hawk) on the standard difficulty or higher, you get a picture of him holding a pistol. In F-Zero GX, you can unlock mini-videos featuring the drivers by beating a cup on the Master difficulty, and I know of at least two, those of Pico and Don Genie, that feature realistic guns.

Kind of funny that they didn't give Snake in Super Smash Bros: Brawl any realistic guns, for the sake of being kid-friendly, when at least three Nintendo characters have wielded them.

Super Mario Bros: Yes, SMB. Not in the game itself, but the instruction booklet, that said that Bowser killed Peach's father by slitting his throat, and that all the blocks players have destroyed with reckless abandon were actually the inhabitants of the Mushroom Kingdom. All of that of course has been omitted by Nintendo. Then again, there's one part in Mario & Luigi that I clearly remember, where scary stories of people getting skinned alive are mentioned. Not that we actually see any of that, of course, but still.

Earthbound: Only one word, or rather, a name, required: Giygas. Really, just enter the name on Youtube, and you'll see. Not the only example from that series, but easily the best one.

Legend of Zelda: Ocarina of time: The golden cartridge version feature a little blood in the fight against Ganon. It's been censored into green blood in other versions. And generally, the series doesn't shy away from mentioning Ganondorf's murderous nature.

Metroid; like the LOZ series, it's not shy about mentioning death. Ridley did kill Samus' biological parents, not banish them to some other dimension or anything strict censors would cook up.

Punch Out: Vodka Drunkenski. Even when they changed his name to Soda Popinski, they didn't bother removing his blatant references to alcohol in his quotes.

Donkey Kong 64; Nothing major, but the word "hell" is used in the DK Rap during the intro. I heard that apparently caused a stir.

I did read somewhere that there was an Hentai game for the NES that was only released in Japan. There's the Gamecube version of BMX XXX, which was uncensored, unlike the PS2 one. I've also heard that the SNES version of MK1 was censored by Nintendo of America, not the original Japanese branch. Does anyone here have any examples of their own?