Check out Mother Brain from the Metroid series.
What other brains are featured in video games?
Even not taking into account all the stories about zombies and brainssss, there is a giant brain-in-a-jar in Baldur's Gate II. It is the boss of the mind-flayers.
the first boss in salamander!
click my name to see.
Dead Head Fred is a game where the main character has his head removed and replaced with a brain in a jar.
Great game for the PSP, dark and funny... and starring the voice acting of John C. McGinley of "Scrubs" fame :)
Don't forget Krang from Teenage Mutant Ninja Turtles! Not sure what game (if any) he was in, but certainly a main character of the series...
Aren't we all forgetting Andross's brain in StarFox 64? Apparently, brains are highly resilient outside of the cerebellum.
There's lots and lots of brains in the Destroy All Humans series. In the first two, you need to use your superior alien telepathy to make human brains explode out of their skulls to collect alien DNA.
And the brains are a lovely turquoise colour when they pop out.