Of the original film franchise, I'd have to say Zod made the best impression out of all the villains, even then. He's a physical equal to Superman and has none of Kal-El's compassion for humankind, and Stamp played that pretty effectively.
I can see where people have problems with Hackman's portrayal of Luthor these days, but in terms of main heavies I'd say he's easily second best of the bunch, simply because of the charisma that Hackman brought to him.
Now as far as the henchmen/subordinates go, again I have to lean toward SII here for my top pick, a tie - Douglas and O'Halloran as Zod's backup are pretty good at being formidable, yet also bringing little touches of humor in each their own way in slight contrast to Zod.
The second best hench, though? Vera Webster. Annie Ross is one of the few aspects of SIII I still like, outside of the Clark-Lana subplot...she's just gloriously b****y, and for lack of giving us a proper Brainiac turning her into a killer cyborg in the climax was the topper.