I have two today:
The barn scene between Clark and Lex in Onyx, culminating in Lex's best line ever, "I am the villain of the story." This scene was an acting tour de force for Michael Rosenbaum, and it must have been a joy to play for him. Lex is smart, ruthless, and invincible in this scene, and puts voice to all the injustices he has suffered at Clark's hands. Clark is confused, frightened, and desperate to have the "real" Lex back, and when he attacks Lex, choking him, he displays a level of passion never seen in his interactions with other characters on the show. Talk about the stuff of legend!
The scene in Spirit where Martha is possessed by Dawn, and she and Clark talk about the prom. Annette O'Toole is beyond hilarious in this scene! OMG, the dancing, her line delivery, her facial expressions - I just laugh and laugh and laugh! And Clark's reactions are perfect - Tom's comedic sense is wonderful! My favorite line? "I'm just super pumped about prom!" I love it! :)