Part 1
Micaiah using Sacrifice on Nico.
Prisoners being thrown into the swamp.
Soldiers cheering for Micaiah.
The entire scene in between leaving the chapter 9 base and the first player phase.
Pelleas being crowned.

Part 2
The scene right before the Prologue starts (when they are in the sky).
Lucia's kidnapping.

Part 3
Zelgius/Skrimir fight.
Kilvas destroying Phoenicis. (This would have easily been the best scene in the game).
Houses being set ablaze in chapter 9.
Elincia/Mercenaries/Valtome scene in chapter 10.
Pelleas being stabbed by Micaiah OR
Pelleas being stabbed by Tauroneo OR
Micaiah being stabbed by Tauroneo.
Sanaki/Micaiah Galdr.

Part 4
Reyson using Galdr on Serenes Forest.
Reyson using Galdr on Renning.
The giant battle outside of the Begnion tower (only available if all allies survive.)
Zelgius removing the Black Knight Helmet
Zelgius dying.
Deghinsea dying.
Sephiran dying.

Anything else?

Dang, I must not have been paying attention in the game I was playing. <.<

The first is only available in 2+ playthroughs and the second one... well, I guess you weren't <_<