I don't know about best moment, but there is a scene that always stuck to my mind.
During G1, there was a 'rogue' Thahd hiding in the woods. It's gained sentience after a life of slavery. It spoke in baby-ish terms, and terrible grammar. Still, I could understand its feelings, its plight, its desire for freedom.
Throughout most of the game I held on strongly to Shaper beliefs of stability and strict control over Shaping. My Shaper dogma wavered at that point in the game.
I killed the Thahd, but not without it planting a seed of Rebel philosophy into me. I would gradually change after