This is definitely a tough question to try to answer. There are just so many.
Bioshock Infinite - The initial time I played through this, it was completely out of the blue. The fact you are Comstock and they just info dump on you about parallel universes; it's all complete insanity.
Half Life 2 - The ending with G-Man is fantastic, the possibility for HL3 were, or are I guess, endless.
Assassin's Creed 2 - It all circled around to an ancient civilization , and opened the door to so many opportunities for the story direction to go.
Portal 2 - It's hard not to love the ending to this game, it's packed full of songs and the consistent humor of the entire game. Spaaaaaace!
Red Dead Redemption - Well, the death of the main character was a completely unexpected event, leading to a genuine 'what the fuck' moment.
Enslaved: Odyssey to the West - Classic tale told with a post apocalyptic perspective. The ending is pretty crazy, dealing with some Matrix style enslavement of humanity and the freeing of minds.
This is a tough one for me. I'd have to say my favourite this year is the Walking Dead, but close behind in no particular order: Fez, Darksiders 2, Trials HD, Binary Domain (this creeped up on me), and Journey.
when it came to storming the gate it FORCES you to use the phosphorous. If you wait too long then the soldiers just start shooting at you and since there is no ammo on the balcony where you are, there really isn't a way around it.
As for the part where the civilians kill Lupo, well if you fire in the air then they disperse.