The 1990's game of the decade is The Legend of Zelda: Ocarina of Time.
The runner up is Final Fantasy VII.
The master thread for all of these contests can be found here.

It is time to vote for Game of the Decade!  A "Game of the Year" has been decided for each year of the 1990's by your votes!  Now, please comment on what you game voted for "Game of the Decade" and why.  These are the 10 candidates:

Super Mario World (1990, SNES)
The Legend of Zelda: A Link to the Past (1991, SNES)
Sonic the Hedgehog 2 (1992, Genesis/Mega Drive)
Doom (1993, PC)
Super Metroid (1994, SNES)
Chrono Trigger (1995, SNES)
Super Mario 64 (1996, N64)
Final Fantasy VII (1997, Playstation)
The Legend of Zelda: Ocarina of Time (1998, N64)
Age of Empires II (1999, PC)

Voting for the 1990’s Game of the Decade will end on Monday, Oct 23 at 11:59 PM, EST.

Great list of games, 5 of which are in my top 50 games of all time list. Chrono Triggers' my favorite game of al time, so easy pick for me here.

Damn. Seven of these are in my top 50. Three are in my top 12.

But I have to go with Super Mario 64. Stellar gameplay and controls. Legendary music. Exceptional ingenuity and artistry. And a giant leap forward for gaming.

Chronic Trigger

Super Mario 64. Still great and just such a groundbreaking game.

1. Final Fantasy VII
2. Ocarina of Time
3. Age of Empires II
4. Doom
5. Chrono Trigger

My actual top 10 is something like this:

Yoshi’s Island
Baldur’s Gate
Heroes of Might and Magic 3
Final Fantasy VII
Ocarina of Time
Flashback
Heart of Darkness
Star Fox 64
Age of Empires II
Total Annihilation

Honestly, I don't really find any of the games from the list to be something I would pick as game of the decade (though I really like some of them), but out of the games that are on the list, I have to go with Doom for being one of the most influential games of all time that resonates to this very date.

Roughly... Final Fantasy 7 > Ocarina of Time > Super Metroid > A Link to the Past > Chrono Trigger >> Sonic 2 > Super Mario World > Doom.

Barely played Age of Empires and I don't remember which part it was. Not a big fan of the iconic Doom or 1st person games in general (my favorite Doom is the controversial Doom 3). Never played Mario 64, and only played Super Mario World for a few minutes.

FF7 to Chrono Trigger are all top tier to me.

I gotta go with FF7, it's pretty damn high on my list of favorite games, top 15 last I listed them. Half-Life might be kind of close (though I prefer the remake of that one), but probably nothing else.

I'll try to do a full top 10:

1. FF7
2. Half-Life
3. Ocarina of Time
4. Pokémon Gold/Silver
5. Symphony of the Night
6. System Shock 2
7. Silent Hill
8. Chrono Trigger
9. StarCraft
10. Super Metroid

A lot of great games on the list, but only one of them is in my all-time top 20, that being Final Fantasy VII. There are other games I would consider better from the 90's, but they obviously didn't make it through the previous round.