Shiguru Miyamoto didn't want to make Ura Zelda (essentially an upgrade or expansion pack) for Ocarina of Time, as he knew that the Nintendo 64 Disk Drive was going to be a massive failure. So, he struck up a deal with the big heads at Nintendo. If he and his team could make a new Zelda game by 2000, they wouldn't have to male Ura Zelda. The deal was made and the result is what we know today as "The Legend of Zelda: Majora's Mask".
The first ever concept art of Sonic the Hedgehog was drawn on a napkin, and he was, at the time, called "Mr. Needlemouse".
Megaman is blue, because the Nintendo Entertainment System had more shades of blue than any other color. Which is odd, considering his sprites didn't have that many shades of blue.
Mario wears overalls because that made it easier to tell what everything on him was (arms, legs, etc.).
An early concept of the characters Ratchet & Clank involved a reptile-like alien with three robot sidekicks.
The Doom Marine is supposed to be YOU!
"Hail to the King, Baby!" did not originate from Duke Nukem 3D. Nor did a lot of the things he said in that game, which so many people credit him for, anyway.
Stop 'N' Swop doesn't actually do anything.
The "Donkey Kong" we saw in 1981, we now know as "Cranky Kong".
Nintendo has used "Zelda's Theme Backwards" at least twice. Once as Midna's theme in Twilight Princess and again as the main theme of Skyward Sword. Aside from the three main notes, neither of these tunes really sound alike.
The Spy was added into the classic Quake mod, Team Fortress when players complained about a glitch that got certain characters' sides mixed up.
A reference to Dr. Eggman from the Sonic series is pretty much the very first thing spoken in the game, Beyonetta.
Although Disney didn't actually acquire the rights to these characters, Mario is mentioned in Wreck-It Ralph and Luigi can be seen in a bar. (His face isn't shown, though.)
Borderlands 2 has a lot of references to My Little Pony: Friendship is Magic built right in.
Between the DreamCast and GameCube versions of Sonic Adventure, the only difference between the intros (aside from the title logo near the beginning) is Tails' mouth. It's closed in the DreamCast version and open in the GameCube version. (This isn't an in-engine cutscene. This is a pre-rendered video, which makes this even more strange.)
In Viewtiful Joe, when Joe plucks out a bomb out of thin air and bounces it on his foot like a soccer ball for a few seconds, he whistles the first six notes of the Super Mario Bros. overworld theme.
In Super Smash Bros. Brawl, the first appearance of the character (not playable), Shadow the Hedgehog is mistakenly labeled as "Sonic Heroes". His first appearance was actually in Sonic Adventure 2. Similarly, the guide says that Sonic can transform into "the mighty god, Super Sonic." It's actually supposed to say "gold", or rather "golden". In fact "Mighty Super Sonic" would've been just fine.
Dolphins are an important theme in Super Mario Sunshine for the Nintendo GameCube (like Delphino Island). Why? Because, the GameCube's prototype name was "Dolphin".
The creator of Earthworm Jim also made a TV show called "Catscratch".
Paper Mario was originally going to be called "Super Mario RPG 2". However, when Square merged with Enix, that broke their ties with Nintendo. So, Nintendo had to make certain changes or remove certain things altogether that Square had involvement in. What's especially bizarre is that the game already had its trademark "paper" look before the name was changed.
In the Sonic series, Shadow was originally going to be called "Terios" (which is Japanese for "Reflection of" or "Therefore, I am..."), Rouge was originally going to be called "Nails" (as part of the rivalry between her and Knuckles), and Silver the Hedgehog was going to be "Venice the Mink". (He also had a yellow mane and went through all kinds of sci-fi gear, including a helmet.)
Skyrim is the fifth major installment of a series called "The Elder Scrolls", which has been around since 1994.
The Legend of Zelda: Ocarina of Time almost got a "T" rating. Not because of the Shadow Temple, the redeads, the deadhand, the bloody walls and floors, or anything remotely-related to that. It almost got a "T" rating because Link thrusts his sword straight into Gannon's face. The ESRB stated that if the graphics had been better, they would have given it a "T" rating. (Note that this was about seven years before the E-10+ rating existed, hence the rating of Ocarina of Time 3D.)