The Mushroom Kingdom prevailing over the Koopa Kingdom, though it turns out that they didn't need to lift a finger against the Koopas since they were innocent the whole time.
Luigi pulling out a Stopwatch and Taking the Bullet for Mario, living long enough to tell him the truth. This single action changes the course of the entire story for the better, and prevents the beginning of Part 1 from happening. And the kicker? Unlike Mario in the dream, Luigi ultimately survives.