Hmm, everytime I think of one good scene another that was way better comes to mind, but I'll try to limit this.
1) I liked the graveyard scene in the pilot, especially the beginning when Lana asks who's there and when Clark replies, he's standing in front of a statue of an angel and all you can see are the wings behind him. I've always loved that shot, and their conversation afterwards was great too.
2) Like everyone else, I liked the flight scene, but my favorite part was definitely the line "I am Kal-El of Krypton. It is now time for me to fulfill my destiny." I get more goosebumps everytime I see that part than the actual flight itself.
3) "Rosetta" - TW and Christopher Reeve, 'nuff said.
4)The final scene of "Metamorphosis" and "X-Ray". I really liked how they captured the emotions of Clark when, even after he fought off somebody who kidnapped her and eventually rescued her from whatever trap they put her in, he can't do anything else but watch Lana run into the arms of Whitney. I especially liked the dialogue between Martha and Clark at the end of "X-Ray" ...
Clark: "Mom, what would you do if you could see everything?"
Martha: "I'd learn to close my eyes."