Season 5- Lex finally starting to really come about and start to assert himself.
Season 6- Lex finally getting to Clark and REALLY making life hell for him. Add in the Lex and Lana relationship and it could easily be nnumber one and on other days might be.
Season 4- "I am the villian of the story" - My second favorite episode behind Lexmas.
After those three it's a toss up and could go many different ways.