Phantasy Star IV for the Genesis is probably the quintessential JRPG I grew up playing. I got it around the same time as III, and I liked it more, but III had an interesting, if not well-implemented concept. It was also the last true Phantasy Star, before they moved on to moneygrab MMOs.
Final Fantasy VII came later, of course, and I still go back to play it from time to time.
I also loved Might and Magic II: Gates to Another World for the Genesis, as it was a more traditional DNDish RPG, and it also introduced me to the magnificent concept of breaking a game via the cheated equipment options. I still have the full size booklet that explained everything, as much of the information was not documented in-game.
Command and Conquer: Red Alert was the first RTS I recall playing at a cousin's house, and that put me on a long road of loving strategy games in general. Particularly because of the Soviet tesla troopers, which were very entertaining. Though that may have been 2, it was released in 2000.
Starcraft, which also had similar effects to the above, along with being endlessly entertaining due to the custom maps, which I also tried my hands at creating, sort of starting my drive to want to become a programmer.
Most other memorable games tend to be in the 2000-2005 range, at least for me.