Bowser
Sephiroth
Dr. Eggman
SHODAN
I feel like that gets the full web of villains in their most defining forms - big scary monster/dragon, JRPG-centric final boss, the mad scientist archetype who's more a minion spawner than anything, and the overwhelming, psychologically taxing presence. I do feel Ganon is just a bit redundant with Bowser there, and in anything else he could be credited for like a puppetmaster or overwhelming force of evil, he's outstripped by someone else who could be on here. SHODAN or GLaDOS is a solid toss-up, though.
Mario Vs Cloud 2002: A Video Retrospective - https://youtu.be/1dx4t6H_K9Y
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