Metal Gear Solid 3 : in the end I had plenty of tears in my eyes for the first time playing videogames.

Shadow of the Colossus: If you have played it, you know how it ends.

Fragile Dreams farewell ruins of the moon: Hands down the game with the most sadness in it ever, from beginning to end.

999: Nine Hours, Nine Persons, Nine Doors : This one has the most fucked up story ever in a very good way, there is simply no game with a better story or anything for that matter. In the final ending my head exploded and my jaw dropped in ways I could not believe it could drop.

Chrono Trigger : My favorite game of all time and when it ended I was both happy with the ending but sad it had to end, but of course I went on to get every ending.

marios face in 3d for the first time aswell

Understandable, I felt the same way bout Nei in PSII. I remember stalling on PSII for the longest and leveling Nei like a dumbass to see if she'd survive. Of course then they killed Alys in PSIV, and I saw that one coming. I always hate how they kill characters in JRPGS and the life restoring items suddenly stop working -_- Let me stop before I go off on a tangent.

Halflife 2, when your climbing the bridge. The most immersive moment I've ever had in a game. The groaning and trembling of the old bridge. The sounds of the sea below you...

MGS4 Shadow Moses dream and flashbacks = best gaming experience ever.

All MGS games are full of emotions. 

The ending of Clannad (there are like 20 endings).....if your open minded enough to play a like it then trust me you will cry your soul out :(

I was awestruck by the beauty of UC2 and while I was playing Flower I started crying.

Pure emotion in games? These:

Half-Life 2 and Episodes 1 & 2: Very much all of Ep 2 was shocking and emotional, especially the end. But also simple moments in Half-Life 2 like seeing the distress of the people in City 17 and getting the crowbar for the first time.

MGS 3 & 4: The Metal Gear Solid games are full of emotional moments, but the ending to these two are particularly emotional. Seeing Snake in the state he's in after following his character over the course of games.

Shadow of the Colossus: Has to be played. It's difficult to convey in words alone.

Final Fantasy VII: Two moments: The point where Red XIII finds out the truth about his father and the "Aeris" scene.

Portal: Pure genius.

Deus Ex: The mood and atmosphere in this game is just fantastic.

Now, if we include anger then a lot of games would have to be included.

There's a lot of them, but in the current generation?

Let's see:

- Portal

- Valkyria Chronicles

- MGS4

- Fragile Dreams

Modern Warfare 2 when Ghost and Roach get shot by Shepherd. Ghost was really the only decent character in the game along with Soap, so I was sad when he died. And I had liked Shepherd before that :p