In order:

Ico
SotC
Journey
Portal
Mass effect 1
HL2 episode 2
MGS4
Papa & Yo
The unfinished swan
Heavy rain

I thought the whole game was fantastic

Yup, totally agree. The ending to Ghost Trick was mind-blowing, to say the least. I still have to try out Virtue's Last Reward, I thought 999 had a pretty cool ending (The true one, of course).

I'm gonna say Phoenix Wright: Trials and Tribulations, just because Shu Takumi rocks.

People seem to disagree, but I will always love the Bioshock 1 Hero ending

Really?? Goddamnit!! I was almost at the end when an update went bad and all of my local content got delted now I have to start the game from the beginning >.<

Well, that's a shame. The last chapter is heavy on story (The final puzzles are pretty easy, but they are there to move forward the story itself), but it's incredible. Really, I couldn't see the plot twist coming, even there's lot - LOT - of foreshadowing about it when you think back everything you did.

Ico
Bioshock
Portal 2
Halo Reach
Mass Effect
Mass Effect 2
Mass Effect 3
Knights of the Old Republic
Zelda Skyward Sword
Tomb Raider Underworld
Panzer Dragoon Saga
Metal Gear Solid

Bioshock Infinite
Metal Gear Solid 1, 3 & 4
Mass Effect 1, 2, & 3 (yes, even 3 with the expanded DLC)
Half-Life 2: Episode 2
Final Fantasy VII
Portal 1 & 2
Deus Ex

Three words, Super Mario Galaxy. The Lumas, was so... so... NOOOOOOOOO!!!

Event in recent days, I wake up in the morning throwing that lament. It was so unexpected in a game of this type.

Mother 3
Chrono Cross
Xenogears
Xenoblade
Bioshock 1 and 2
Zelda: Skyward Sword
Arc Rise Fantasia
Golden Sun: Dark Dawn (Gimmie a sequel damn it!)
Batman Arkham City
Fire Emblem Awakening