Bah, I'll just go through the top 10 and see if I agree.

Top 10
10. Andrew Ryan from BioShock
9. Mother Brain from the Metroid series
8. Psycho Mantis from Metal Gear Solid
7. Inky, Binky, Pinky, and Clyde from Pac-Man
6. Those damn Nazis from every game based on WWII ever.
5. Donkey Kong from... Donkey Kong
4. Sephiroth from Final Fantasy VII
3. Ganon/Ganondorf from the Zelda series
2. Bowser from the Mario series
1. GlaDOS from Portal

Anyway, I'm surprised at the top pick for this list. Now for the next four making up the top 5, not so surprising really. I was kind of expecting Sephiroth to be listed at 2 perhaps, but 4 seems alright, even though he deserves a much lower spot than in the top 5, and the others are pretty much classic Nintendo villains. I don't know why IGN listed the Nazis, but they shouldn't count at all. :P

I'll go ahead and check out the other 90 picks I skipped.