My would be:
1 - Suikoden II (PS1)
2 - Final Fantasy VI (SNES)
3 - Metal Gear Solid (PS1)
Suikoden II for me was the best story in an RPG ever. It felt so epic how this two best friends who wanted the same thing but went in completely different ways and the ending (if you get all 108 stars) is amazing. The song in the opening is also awesome.
Final Fantasy VI was the best Final Fanatasy for me. Since IX, I dont know what happened, but I really dont like the story in the Final Fantasy and XII was the first one I didnt finish because I didnt care anymore.
Metal Gear Solid was a game that I didnt know when I bought. I only bought it because I really wanted to buy a game so I wouldnt go home empty-handed and it turned out to be a great game with really cool bosses and history.
Honorable mention - GTA III. A game that was revolutionary at the time and provided countless hours of fun
(and the also great sequels Vice City and San Andreas).