I voted for season 5. It was the writing was the most complete all around. The actors and fully settled into their roles and hadn't yet started their aimless meandering of later seasons.
Marsters was great as Brainiac, and the Lex/Lionel clash was at it's best as both were amidst a transition.
I also think "Hidden" is the show's single best episode. It didn't fall into any of the traps the show was famous for. Mack and Glover were both absolutely brilliant, and it was the time where Welling (CGIed or otherwise) most closely embodied the essence of Superman.
"Arrival" was really the one time they did a season premiere right.
My biggest complaint with season five is how badly it represents a bicameral state congress, but I digress...
Season 3 loses points for not keeping Morgan Edge around more. Plus, replacing Rutger Hauer with Pat Bergin is a felony in some countries.