Aang (Avatar: The Last Airbender) use Energybending to eliminate one's bending abilities.
As the progenitor of all Quincy, Yhwach (Bleach) can grant and take away their powers as he sees fit.
Through severing and manipulating someone's true name, Ichibē Hyōsube (Bleach) can remove the powers of anyone he hits.
Alex (Misfits) gained the power to remove a person's power through sexual intercourse after having a lung transplant from the previous owner of the power.
Penny (Charmed) with the power stripping potion.
Mikan Sakura (Gakuen Alice) can permanently steal an Alice at will or by accident.
Tommy Clark (Heroes Reborn) erases Hiro's power just by being held by him.
Amon (Avatar: The Legend of Korra) can use Bloodbending to sever the connection between a bender and their bending abilities by disrupting their chi paths.
Enrico Pucci's Stand, Whitesnake (JoJo's Bizarre Adventure) can remove the Stands of others, storing them in discs. It also makes it able to bestowal these Stands upon others by inserting the discs on them.
Through a contract, Hades (Disney's Hercules) erases Hercules' superhuman strength.
Mojo Jojo with the Antidote X (The Powerpuff Girls)
Edward Brock/Anti-Venom (Marvel Comics) tries to cure Spider-Man of his radioactive blood and his powers...
...and attempting to "erase" the Venom Symbiote from Mac Gargan's body.