Viktor. What's scarier than a mad scientist who turned himself into an early cyborg and wishes to do the same to everyone else, which also turns his victims into mindless followers? As for those listed:
Swain- As far as I can tell, Swain has never done anything outright evil, even though he is now leading Noxus. He strikes me as a powerful leader who is harboring a certain secret.
Malzahar- If Malzahar gets the Void unleashed onto Valorian before Viktor begins his "glorious evolution", then he would be bad guy #1, no denying that.
Mordekaiser- Doesn't strike me as someone who is out to conquer the world. I don't see anywhere in his lore any furher ambition from him. I'd say he is just a hulking, undead baddie, but not a world-destroying evil.
Veigar- A single mage who wants to destroy everyone. Considering the scale of his goal, I doubt he can truly conquer all of Valorian.
Varus- As far as I can tell, Varus doesn't spread the corruption as long as he is in control. Once he loses control, and if it is before Malzahar or Viktor enacts their plans, he would become the true evil.
A final thought: What if everyone with an overarching plan starts their plot at once? You can't really call any evil the big one until it starts winning >.< (not to say they aren't evil)