User is an entity completely comprised of a brain or multiple brains, is a disembodied brain in a synthetic body, or they could be completely be formed from brain-matter and/or aspects of the nervous system. This could count as a literal meaning, their physiology looking and behaving just like a regular brain, or this could be symbolic, their physical form a manifestation of their brain.
The Invisible Creatures (Fiend Without a Face) are monsters made of pure thought that physically feed on the brains and spinal cords of their victims, their physiologies resembling brains and spinal cords.
The Brain (The Brain) is an alien organism that can psychically tamper with the brains of normal human beings, the creature itself resembling a giant brain.
The Brain Spawn (Futurama) are living brains with the power to reduce others' intelligence.
The Divine Predecessors (Lexx) are the extracted brains of the former Divine Shadows, retaining all of their memories and knowledge.
The Brains (Jimmy Neutron: Boy Genius) are a race of brain-like aliens with limited psychic powers.
After his body was destroyed in a bomb blast, Hector Con Carne (Evil Con Carne) was reduced to a sentient brain.
The Brain (DC) truly lives up to his name.
Dr. Wheelo (Dragon Ball Z: The World's Strongest) is a disembodied brain in a robotic body.
At the end of the game, it is shown that all that is left of Ruvik (The Evil Within) is his brain, his mind literally hooked into the main circuits of STEM.
Mother Brain (Metroid) is an organic supercomputer in the shape of a giant brain.
Aurora Units (Metroid Prime 3: Corruption) are brain-like organic supercomputers used by the Galactic Federation.
After a brutal battle with Samus Aran, Weavel's (Metroid Prime Hunters) brain and spinal cord were placed into a cybernetic body to preserve his life.
Tainted Wisdom (Yu-Gi-Oh!)
Brain Golem (Yu-Gi-Oh!)
SCP 1027 - Carnivorous CNS (SCP Foundation)
After repeated injuries at the hands of the Shredder, Baxter Stockman (Teenage Mutant Ninja Turtles) was eventually reduced to a disembodied brain.
Utrom (Teenage Mutant Ninja Turtles)
Krang (Teenage Mutant Ninja Turtles; 2012 TV series)
Douglas McNoggin (Lloyd in Space)
RoboCop 2 (RoboCop) is operated/powered by the brain of the deceased drug lord Cain.
The Brain of Mensis (Bloodborne) is a grotesque, brain-like entity and a powerful Great One.
The Aurum Brain (Kid Icarus: Uprising)
Brain Pods (Buzz Lightyear of Star Command)
Ego (Marvel Cinematic Universe) is a celestial who's true form is a brain, having learned to create a planet and a human form using matter around him.