Most of my favorite scenes throughout the trilogy are all in Part II:

- The flashback "Surprise Party" scene at the end of the film
- The flashback story of young Vito (all the scenes, actually)
- The scene where Michael tells Fredo he "broke his heart"
- The scene where Kay tells Michael that she is leaving him
- The scene where Kay leaves

But I think those are just "current favorites" because I just saw Part II last night and I still have to refresh my memory about the other two films.