Seeing Lelouch take the throne and then Geass all the royals into obeying him...Just seeing him and Suzaku smile as they took over all of Britannia in one fell swoop was epicness. And everyone's shocked reactions just made it even better. (NO ONE saw that one coming, I do believe.
)
There were tons of other scenes I loved, but I think the other one that sticks with me the most is the scene with C.C. after the end credits of the last episode of the first Season. Her thoughts about Lelouch's life and motivation, and especially about humans in general, really put things in perspective for me, I find.