Braid.

That's a hard call, but I'd be really tempted to go with Big Red Racing or possibly Lode Runner: Mad Monks revenge.

Hard choice for me too, lots of candidates. I think I'd have to go with Heroes of Might and Magic 3 though, since that's the one that really got me into gaming.

On PC:
Jagged Alliance 2 / Baldur's Gate 2

On consoles:
Persona 3 / Persona 4

It's impossible for me to choose only one... :(

Anstoss 3, a german football manager from Ascaron. From the series only the first was released in english as On The Ball. Just close behind is Civilization 2. Both series (Anstoss 1-3; Civ 1-4) wasted years of my life ;-)

Probably Ultima VII, but Final Fantasy VI, BG2 and Fallout 2 are not far.

I can not choose just one when so much could fit into that category...

... but there is one that often comes to mind when I think of my early playing days and I remember with special affection: Loom (a Lucasfilm's adventure game with a truly innovative control system and a story that I loved from the beginning

Hard to chose between Torment, Bloodlines & Thief.

Civ4

Processing.................................................................................................... .................................................ding!
Super smash bros. Melee. It's addicting and SO fun.

I could never restrict myself to a single favorite title, but a (very incomplete) list would look something like this:
Wizball (C64)
Moonstone (Amiga)
Deuteros (Amiga)
Civilization II
Dungeon Keeper
Star Control II
Diablo II
Settlers II
Heroes of Might and Magic II
UT2004
Warcraft II

I think it's interesting to note how many games on my list are specifically the second installment in a series.

Secret of Mana (SNES)

I can't even make my mind up what favourite game means(to me). I guess the fairest way to do it is by the amount of time invested. With that said the winner is...

Rise of Nations

Pretty much all the game from my childhood :

worms, the secret of monkey island, arcade america, x-wing alliance

And 'recently', dragon age origin

Mostly SNES games for me.

Chrono Trigger
Super Mario RPG
Super Mario World
Super Mario Kart

And No One Lives Forever for PC. We need this one gog! Do it!