Impossibile to pick a single game from that era

I would say Dink Smallwood

Ocarina of Time Hands down. That was the game that redefined the open world game and took one of the best Nintendo IPs and fleshed it out in 3D in ways that nobody thought possible. It also pushed the N64 hardware to it's limit and really showed what the system could do. The game is beautiful, atmospheric, understated and at the same grandiose, intuitive and pleasingly difficult. A legit masterpiece...

Chrono Trigger.

Still my favorite JRPG. Where other games like Metal Gear Solid and Ocarina of Time have aged to some extent or another, Chrono Trigger remains truly timeless.

Donkey Kong Country - everything about the game is marvelous, from the graphics/atmosphere to the music, solid mechanics, appealing gameplay. Perfect balance of simplicity and difficulty. I'd actually probably throw DKC2 in here as well. While it wasn't quite as iconic and charming, Rare fleshed out the gameplay and difficulty making for a more thrilling and in-depth experience. Some of the best music in gaming on both fronts too.

Secret of Mana - super fun, rich, action-packed RPG that's a blast both in single and multiplayer

Mario RPG - my first RPG and still my favorite (along with Secret of Mana). Just a super satisfying, addictive game with really fun combat and some amusing story/dialogue.

Late SNES era stuff is my jam so maybe I'm a bit biased but those are far and away my favorites of the decade. 

Technically it's The Legend of Dragoon for me, sinceit was released in Japan in the 90s, but it didn't come out in Europe until 2001. If we don't count that, then it's Freespace 2.

See people have mentioned a lot of great games already, I'll throw in Baldur's Gate.

Super Metroid. Still a masterpiece 25 years later. Not many games can pass the test of time as well as this one

Age of Empires II, by far. The best RTS ever made to date.

Other great games were Pokemon Red/Blue, Chronno Trigger...

Chrono Trigger, Suikoden 2, FF6, A Link to the Past, Super Metroid, Ocarina of Time. Too many of my favorite games came out in the 90s, I dont think I can choose 1 game as "game of the decade".