Well fuck, this about sums up what I came in here to say

Right off the bat... not one, or two or 3 but 7 games come to mind as my all time faves. Sorry, its not just one.

- Metal Gear Solid (PS1) [first game I played that was a game and something else]
- Ocarina of Time (N46) [this is what an adventure RPG should be. Plain and simple]
- Zone of the Enders: The second runner (PS2) [best mech game ever. Till date, no mech game has come close]
- Gran Turismo 3 A-Spec (PS2) [this game set the bar that til date every racing game is trying to beat, GT included]
- Shadow of the Colossus (PS2) [I doubt there will ever be a game like this again. They should remake this game]
- Vanquish (PS3) [Pure, balls out, all guns blazing, dynamic, I am unstoppable action. Perfect]
- Uncharted 2 (PS3) [ I sat down to play this game, and didn't get up till it was done. Didn't realized its been 20hrs]
- The last of Us (PS3/PS4) [I feel bad for anyone that hasn't played this game]

Oops, that was 8!!!! Can't blame me, theer have been some really great games, and they all impacted me differently.

Saints Row 3 and Saints Row 4 in particular fit this bill :)

Guild Wars 2 for me. For console games I'd pick Star Ocean 2.

I'd say Uncharted 2.

That's a good question. Let's take a look at the top:

Looks like Mario Kart 8 takes it.

First game that came to mind would be Arkham Asylum. City may be better overall with more things to do, but Asylum is a much tighter experience. The narrative is focused and while it may have been much smaller they made better use of the space they had in the game which led to better pacing and a better balance between combat and predator sections.

Ratchet and Clank but I'm not sure which one. A Crack in Time I guess as the humor was just crazy sometimes and it just made me feel really kid like.

Crash 3 is still a blast as is Uncharted 3 every time I go back to play it.

I already differentiate what I consider my favourite game (which seems to be what you're asking) and best game ever, so my favourite game is Wind Waker. I don't necessarily consider it the best made Zelda game, but it's definitely the one I've had the most fun playing through, all 6 times I've done so. :P And I think that's what's most important in choosing my favourite game, the one I enjoyed playing the most. People have issues with it that I understand, like the slow travel, but I enjoy it. It's relaxing, and the music while sailing is awesome. Combat is super fun, dungeons are excellent, music is one of my favourite soundtracks in gaming, and I love it all. So I consider it super well made even if others don't, though I will say Ocarina of Time and Link to the Past are probably more well made, but less enjoyable for me (though OoT by only a bit).

TLOUR! Such a delight experiencing this gem!