Mother Brain

Mother Brain is a large, biological computer resembling a cycloptic, spiked brain and the leader of the Space Pirates that appears as a recurring antagonist in the Metroid series of games.

Nintendo Comics System
In the Nintendo Comics System story "Duh Stoopid Bomb!", the name "M. Brain" can be seen on Wooster's list of people who think the Mushroom King is dumb.

Super Mario RPG: Legend of the Seven Stars
Mother Brain is briefly mentioned by Samus in Super Mario RPG: Legend of the Seven Stars, who claims to be "resting up for Mother Brain".

WarioWare, Inc.: Mega Microgame$!
In WarioWare, Inc.: Mega Microgame$!, Mother Brain appears in the microgame Metroid, a recreation of the final boss of the original Metroid. The player, as Samus, must blast Mother Brain repeatedly with missiles and dodge her own attacks in order to defeat her.

Super Smash Bros. for Nintendo 3DS / Wii U
Mother Brain appears as an Assist Trophy in Super Smash Bros. for Nintendo 3DS / Wii U. When she first appears, several Rinkas appear that damage opponents, though, as they are energy-based, they can be absorbed or reflected. After some time she then uses the Laser Brain Attack for massive damage. When she uses the attack, however, the glass surrounding her container shatters, allowing opponents to attack and defeat her.

Trivia

 * In the Brinstar stage seen in many Super Smash Bros. games, a massive brain can be seen occupying the background, often writhing during earthquakes. It is unclear if this is intended to represent Mother Brain, though it does not particularly resemble any form of hers from the Metroid games.