Guenael Lee (Bleach) using his Vanishing Point to cause his own appearance, existence and memory of it to vanish.
Alak-Hul (Destiny) can use the darkness in the surrounding area to in order to vanish.
Iskatu (Diablo) can vanish completely from the battlefield and then reappear at anyplace at anytime.
King Chicken (Duckman) created the Beautex virus, which eats away matter, causing it to devolve through its various stages and then banishing it into nowhere, causing the world to nearly vanish completely.
Jacob Lessio (Fairy Tail) when he claps his hands can cause everyone in the Fairy Tail guild hall to disappear to the point of which they are almost dead.
Jester (Valkyrie Crusade) can make things vanish/disappear, including herself.