This is like my list of strongest anime characters I made a bit back (which, I'm proud to say, has gained a bit of fame around here). Feel free to argue with what I put. To avoid confusion, there'll be no Visual Novel characters here (I''m not even sure if they count as games). They have to have originated from a video game.

1. YHVH (Shin Megami Tensei) - Megaversial Omnipotent; defeated only because it chose to be, came back anyway
2. Wave Existance (Xenogears/Saga) - The Supreme being of the series, but little is known of it
3. Zeedmillenuimon (Digimon) - Multiverse destroying living parradox
4. Perfecto (Super Robot Wars) - Multiversial being
5. Giygas (Earthbound) - Universe+ destroyer; can attack through time and dimensions; the chosen one with Universal Pk couldn't even scratch him
6. Exdeath (Final Fantasy V) - Can only truly die if everything else in existance is destroyed; even in his weaker form he merged two planets into one
7. The Profound Darkness (Phantasy Star) - The Ultimate darkness of the Universe
8. Sheogorath (The Elder Scrolls) - As the Daedric Prince of Order, Jyggalag, he was so great that the other Daedra feared him and ganged up against him to make him Sheogorath, the Daedric Prince of Madness
9. Pyron (Dark Stalkers) - Planet-eating fire-demon that can grow to the size of the Milky Way
10. Amaterasu (Okami) - Celestrial Brush God who can even manipulate galaxies with her power
11. Asura (Asura's Wrath) - Destroys planets and stars with ease; beating Chakravartin could make him much higher
12. Sirius (Megaman Starforce) - Lives inside the blackhole in the centre of the galaxy; can destroy solar systems with his blackholes
13. Maxwell (Scribblenauts) - Strong reality warper who can bring things to life and kill them again with a word and create almost anything, though has only showed solar levels of destruction with blackhole; this isn't including Unmasked
14. Iris (Golden Sun) - Starbuster
15. Overlord Laharl (Disgaea) - Very casual planet buster; someone who has actually played the series can correct me
16. Kirby (Kirby) - Can eat almost anything his size; has a few planet busting feats
17. Bayonetta (Bayonetta) - Kicked a Moon-sized Goddess into the Sun; may have a power boost with he next game
18. Gravemind (Halo) - Galactic Lifewiper
19. Bowser (Super Mario Galaxy) - Moonbuster
20. Lavos (Chrono Trigger) - Casual lifewiper