Theres a few games that i consider to be masterpieces. Sonic 3 & Knuckles, FF7, Chrono Trigger and Chrono Cross, Resident Evil 2 and Code Veronica, Silent Hill 2, Metal gear solid, Suikoden 2, Grandia 2, etc.
But if theres one game i would say got the closest to perfection, its Xenogears.