For me, it's Panzer Dragoon Saga (Saturn 1998). I might have enjoyed some games more than it - very, very few to be precise - but for what it did back in its day there was no way of getting any better. The PD universe is as diverse as it is mysterious, the characters are fantastic, the drama intense - without comic relief EVERYWHERE just because it's supposedly an Eastern RPG - the scenario is serious and full of interesting events and the combat is great.
There is very little to be found in terms of "problems" in this title since it nailed down most of the problems of the genre and addressed them: No insane encounter rate, no endless fetch quests, no tons of obsolete gear everywhere. Everything in PDS had its purpose as much as every and each one of its characters had a specific role to play in the events.
Real shame that so few people got to experience it...