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!!
Signature goes here!
