Creator's Oddball: Metroid is tonally much Darker and Edgier than many of Nintendo's other franchises, featuring bleaker aesthetics and having darker themes such as genocide at the forefront rather than as a background element.
The appearance of the Varia Suit in Metroid II: Return of Samus and onwards is the result of the Game Boy's lack of color. The original NES game had Samus's suits differentiated only by color, but since the grayscale Game Boy lacked such a color palette, the suit itself was redesigned with large shoulders, which would become its trademark.
With Metroid 1, the iconic Morph Ball came into being because the programmers had trouble making an appealing animation of Samus crawling through small passageways. So they made a much simpler animation of a rolling ball.
Stock Sound Effect: Present in both Super Metroid and Zero Mission. Both games make use of a roar originally used in Universal's 1957 film The Land Unknown for the Tyrannosaurus. Kraid uses this roar in both games, while Crocomire and Phantoon share it with him in Super Metroid.
Also present in Super Metroid is Anguirus' roar used for both Draygon and Ridley. It may be due to this that the other roar was mis-attributed to this franchise as well, with the trivia web series Did You Know Gamingsaying that its the monster Titanosaurus.
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 with such a twist.
The Varia Suit was mistranslated from the Japanese Barrier Suit, the Japanese equivalent. The new name was kept for the sake of consistency, but has the bonus of also potentially being short for "Variable Suit", pertaining to its abilities to handle many different types of environments.
Urban Legend of Zelda: Many minor ones, but most well-known are the belief that the infamous Justin Bailey code had an actual meaning, and that a similar code exists in Metroid II and Super Metroid. "Justin Bailey" is just one of many randomly generated codes, some of which grant the same result, and no similar code exists in other entries of the series.
Kraid was going to appear in Metroid Prime and there was even a model ready to be used, but due to time constraints, he was cut out. Contrary to popular belief, however, he was not cut in favor of the Omega Pirate, who was conceived before Kraid was for Prime.
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 (he wanted to go along with the "simpler is better" philosophy used for more casual Wii games while also giving a more NES-like control scheme), the developers were forced to go with the remote only.
In the 2012 E3 Direct showing off the Wii U, an icon representing the franchise is shown. As the Metroid Prime Trilogy port for the system hadn't been announced (and wouldn't be available until 2015), it's possible that at one point, the idea of a Wii U Metroid game was thrown around.
You Keep Using That Word: On a meta level, "bounty hunter". In practice, Samus is more like a freelance peacekeeping agent, in it for justice and righteousness rather than greed or even paying the bills. When Retro Studios tried to include a sidequest where Samus hunted bounties for money in one of the Prime games, Nintendo shot down the idea immediately, with the ensuing conversation revealing that she's basically a "paramilitary contractor", with the closest thing to a bounty being her negotiated paycheck. Using the term "bounty hunter" was Rule of Cool on the part of her Japanese creators.