Fan Nickname: a handful of rooms in Super Metroid, such as "Noob Bridge" in Green Brinstar, and "Mount Doom" in Black Maridia.
Also, Shockness Monster/Serris in Fusion, and Choogle/El Pollo Loco/Little Birdie/ Clone!Ridley in Other M.
Franchise Killer: Metroid: Other M has put the franchise on hold, due to lower-then-expected sales and the controversy surrounding it. Then again, this isn't first time there's been a large hiatus between entries in the series; see 1994 and 2002.
Serendipity Writes The Plot: The appearance of the Varia Suit in Super Metroid and onwards is the result of the Game Boy's lack of color. In the original NES game the Varia Suit was denoted by a change in color of Samus' suit but since the Game Boy didn't have enough color to differentiate, the suit itself became physically different after obtained in Metroid II. The larger shoulders became the trademark of the Varia from then onwards.
Throw It In: The concept of Samus being a woman wasn't used until the last minute when some of the developers thought it would be cool to surprise players that beat the game fast enough would get to see Samus' true gender.
The Varia Suit was mistranslated from Barrier Suit, the Japanese equivalent. The American developers kept the Varia name probably because it sounded cool and to keep the names consistent throughout the series.
The title of the franchise, Metroid, was something else entirely during development of the first game. It was originally going to be called Space Hunters.
Similarly, Crocomire from Super Metroid was going to be in Metroid: Zero Mission. He even had sprites and basic AI ready, but he was Dummied Out for unknown reasons.
Metroid: Other M was going to have the nunchuck be used in conjunction with the Wii Remote, but thanks to Executive Meddling from the game's director, the developers were forced to go with the remote only.