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 El Pollo Loco/Little Birdie/ Clone!Ridley in Other M.
Hey, It's That Voice!: In the Japanese version of Metroid: Other M, Samus is voiced by Ai Kobayashi, who also voiced Deunan Knute in Appleseed movies. This is also counts as funny at first sight, since Deunan and Samus share similar backgrounds and similar screwed-up pasts.
Throw It In: The Evirs' "dance" right before the Draygon boss fight in Super Metroid was secretly added in by Yasuhiko Fujii while the other programmers were asleep, and was intended to reference a woman he was dating at the time (the "dance" traced the letters "Keiko Love" in English).