Alien X (Ben 10) cannot be destroyed by any conventional means. Even when the entire universe was erased, Alien X was the only thing remaining.
The Spectre (DC Comics) survived getting erased on a meta textual level after being thrown into the void beyond all voids
Grand Zeno the Omni-King (Dragon Ball Super)
Future Zamasu (Dragon Ball Super) is completely inerasable due to his Absolute Immortality, making him immune to the effects of Hakai. Only via Zeno's power of Nonexistence was he erased out of existence.
Oblivion (Marvel Comics)
Jack Rakan (Negima)
Chaos (Valkyrie Crusade) is inerasable, and will never cease to exist.