I don't know the exact times but FFX, DQ8 & San Andreas all consumed fractions of my life.

Pokemon Emerald: almost 700 hours, and that's not counting the restarts (not saving because of a screw up). The damn battery in the cartridge ran dry a long long time ago lol. If I count the remakes, then that goes up to almost 900.
Smash Melee would probably be second (I don't know how much time I've put into it, but I've had it for a very long time and still play it so there's that)
Fire Emblem Awakening at around 250 hours in third and Ocarina of Time in fourth.

And now I have realized I spend a lot of time playing games. It's a weird feeling.

Pokemon Diamond (I think) with around 400h playtime on my first file. I've also restarted it several times, so it's likely around 500h. If Pearl and Platinum count towards it as well, it's around 600h.

Edit: I've also spent a lot of time playing Brawl and MK Double Dash. Probably 100-200h for each of them.

Spent over 300 hours on F1 2010.

Probably spent near that on Pokemon Yellow but that was a long time ago so can't be sure

CoD: MW2

I've been plating Metroid Fusion regularly for 13 years now >.

250h Dark Souls

I'm not exactly sure about the game I've spent the most time with, but I've spent at least 200 hours with Quake III, CS 1.6, Smash Bros Melee, Pokemon FireRed, Pokemon HeartGold, Mario Kart DS and a couple of another games!

Shogun 2 from what is tracked with 165h currently and counting each week. Rome 2 comes in a close second with 158h but I've played that shit for too long straight. I always switch between various TW games.

Well I have 1645 hours in TF2 according to Steam.