Such a great decade, many of my Top 50 games come from that era but if I had to choose I'd go with Chrono Trigger. It's the perfect RPG, it has tons of charm, a fun story, a kickass soundtrack, multiple endings, it makes use of the time travel element really well both in the storyline and for the end game sidequests.

As a bonus, here's all the games from the 90s that are among my favorite of all time : 

#1: Chrono Trigger

#4: StarCraft: Brood War

#5: Legend of Zelda: A Link to the Past

#6: Final Fantasy VII

#7 : Super Mario 64

#10: Secret of Mana

#11: Final Fantasy VI

#12: Metal Gear Solid

#15: Final Fantasy IV

#17: Super Metroid

#22: Castlevania: Symphony of the Night

#28: Super Mario World

#29: Resident Evil 2

#30: Donkey Kong Country

#37: Mario Kart 64

#39: Battletoads

#42: Super Castlevania IV

#44: Star Fox 64

#46: Tenchu: Stealth Assassins

#47: Super Punch Out!!

LOL

show me the thesis

Good yes, but I can't put it in my top 5.

Best of the 90's for me would be something like this:

1] FFVII

2] Castlevania: SotN

3] Streets of Rage 2

4] R4: Ridge Racer Type 4

5] Ninja Gaiden II: The Dark Sword of Chaos

The Legend of Zelda Ocarina of Time.

There’s plenty of games in this decade that are easily better than the best games of every other decade though, this was the Golden Age. In my Top 50 I had about 30 90s games.

Ocarina of Time ...no other comes close.

Super Mario 64

For me, Banjo Kazooie.

It took the formula by the already incredible Mario 64, refined and improved it, and added its own charming style. So many of its worlds remains among the most memorable gaming levels for me even more than two decades later, and the game itself would stand as my favourite game of all time until Resident Evil 4 came along many years later.

Really though, I could go on forever about how amazing the 90s were in terms of games, the sheer number of stellar and revolutionary titles is staggering. Other titles like Ocarina of Time, Starfox SNES and N64, and Donkey Kong Country 2 also still count among my all time favourite games to this day.

Tribes for me (after the community modded it with all the mods).

Loved how you could either be offensive player or defensive to protect the base. Engineers could set up shields, satellites, weapon traps etc.

It's not even close. Ocarina of time. From mario 64 to ocarina of time, Nintendo was literally teaching the gaming world how to make good 3d games. Ocarina of time is #1 and mario 64 is #2.

Has to be Chrono Trigger. First time I played the game it was sheer magic.