Spider-Man - When Peter raises his head and throws the trident back at the Green Goblin
Spider-Man 2 - The entire "I'm back!" scene up to where Peter starts to fall
The Amazing Spider-Man - Crane scene (the theme music gets me every time!)
TDK - Batman taking out the SWAT team
DKR - Batman's flaming symbol (Music is awesome here too), Bruce escaping the pit.
There are others, but for me, the music helps make these moments. Good superhero themes played at the right time are uber-effective. These moments to me are some of the best examples of " YES!" moments.