It heavily depends on personal taste and genres. For me, computer gaming always had a massive edge over consoles, all the way from early 80s to this very day, but if I prefferred different genres than I do, it could've been easily the other way around.

There were simply too many great, influential games in the 90's to pick just one. For me it was the best decade for games, period! Pretty much in every year, something groundbreaking was introduced. From whole new genres, 3D games, optical drives, VR to on-line gaming (or simply, the internet).
Even picking top game of each genre, feels like picking your favourite child. It's impossible to choose. Take FPS games for example. We've gone from Wolfenstein 3D, through Doom, Duke Nukem 3D to Quake, Unreal Tournament, Golden Eye, Half-life and Medal of Honor, with tens of fantastic others in between.

Instead here's my top influential games of the 90's.

Fighters: Street Fighter 2,

FPS: Doom

Strategy: Civilization

RTS: Dune 2

Action: GTA

RPG: Fallout

JRPG: Chrono Trigger

ARPG: Diablo

MMORPG: Ultima Online

Final Fantasy VII and MGS1. I can't choose 1 between those two, the quality along with the impact they had feels immense.

Yeah the industry just seemed to move to fast back then with constant revolutions and breakthroughs.

The decade started with the launch of the SNES and ended with the Dreamcast, with the likes of Doom, Quake, Mario 64, Goldeneye 007, Metal Gear Solid, Half-Life, and Ocarina of Time propelling gaming forward in leaps and bounds.

Now that the industry has matured we just don't see this kind of thrilling, volatile roller coaster ride of fresh new miracles any more.

FF7 easily. It's not just a very fun consistently engaging game with great pacing. It didn't just revolutionize the RPG genre but the entire landscape of video games. It was the first game to push the idea out in the mainstream that games could be more than just great gameplay; they could also have stories and soundtracks that can rival and eclipse movies and books. It nails every main aspect that a game can do down at the highest levels as well from gameplay to story to soundtrack.

Super Metroid, followed very closely by Ocarina of Time and FFVII.

Doom

/end thread

Age of Empires II. 'Cause it was my childhood and it's genuinely a great game.

Starcraft.

Everyone who says something different is wrong.