Which video game(s) led you to think about the storyline for at least a day upon completion of the game?

Metal Gear Solid 4

FFX & FFX-2

Metal Gear Solid 3

Ehh I'll add some more later.

Mario Bros.

I always wondered why King Koopa didn't just cut off the bridge while Mario was running at him.

It's what I would have done.

Braid. I still trip trying to understand that one. Also Mass Effect, though more to wonder about where the sequel is headed than to understand the first.

All of the games I own that have a story. Seriously, if a game has a story, then I think about that story while playing. duh...

<_< But there are some games where I question certain parts...

Half-Life 2, Bioshock, Majora's Mask, Wind Waker.

Forget at the end, I think about a game's story the entire time I'm playing it. Though usually only the RPGs have enough plot for much consideration. Xenogears in particular tops that list, mostly because of how they basically condensed the key plot points of five planned games into one game.

Not so much the story, but CoD4 got me obsessed with the SAS for a while.

Mass Effect

Metal Gear Solid(1,2,3,4)
Final Fantasy X
Assassin's Creed
BioShock
Chrono(both Trigger and Cross)
Persona 4

Bioshock and Final Fantasy X