Oh, there are so many! :) Here are three that instantly spring to mind:
1) The scene in Leech where Clark plays pickup basketball with Sam and Whitney. Clark is so carefree in this scene, it's a complete joy to watch. Tom did a great job of portraying Clark as he let the burden of being super-powered slip from his shoulders. Plus the pure athleticism of the action is beautiful, not to mention that white T-shirt Clark is wearing! Yum! Curiously, this is the only scene in the history of Smallville that I've been able to identify where Clark actually wears sneakers outside of gym class, and don't think I didn't use my freeze frame to verify that!
2) The scene in Red where Clark comes into the Talon and kisses Lana. It was so fun to see Clark be truly confident for the first time, and that kiss remains one of the hottest I've ever seen. It still hits me with a physical thrill every time I see it, and with the help of my rewind button, I've watched it more times than I care to admit!
3) The scene in Blank where Clark bends the crowbar, and Chloe tells him about his super abilities. Both Allison and Tom were amazing in this scene! Chloe is wistful and tender, and Clark is vulnerable and confused. It breaks my heart that Blank!Clark can realize in an instant that he can totally trust Chloe with his secret, while Real!Clark still can't take that step.
Yay! That was fun! And please tell me I posted correctly this time!