I just watched the entire fourth half-season online after being ridiculously busy with work while they were actually on air, and I think there were SO many scenes in there...But there are others from other seasons as well. Usually the ones I like best are the ones that make me cry. :P
Season 4: I agree that the scene where Lee leaves Galactica had me in tears (and my boyfriend was laughing at me.) So INCREDIBLY well-acted.
Season 4: . Bill Adama returning, the Adama/Roslin hug, the whole "I love you" moment. *sniff*
Season 3: Helo having to shoot Athena so she could resurrect and get Hera - oh, my gosh, I just can't imagine...having to shoot someone you love...
Season 4: The moment when the troops came to take Tyrol and Anders away, and they tell Starbuck that the two are cylons, and Sam tells her it's true...It wasn't a very long moment, but I think it was SO well acted, and very poignant - just the expression on his face was amazing.
Season 4. The scene where Tory sends Cally out the tube. I was absolutely on the edge of my chair, my hands over my mouth, going "Oh, my gosh, they are actually going to KILL her."