Well... It's difficult to say what's the best but...
1. Ocarina of Time - An amazing gameplay and later on when I learned to understand english better, the story got me. It's the Zelda feeling that makes this the best.
2. Majora's Mask - If this had gotten out before Ocarina maybe this would have been the best... But still it's a great game. Link's personal adventure. It deserves more respect!
3. Final Fantasy VI (SNES) - Well, it's Final Fantasy. A great rpg with great character developement and story.
4. Perfect Dark - Wow! Best fps in the world. Especially the gameplay is stunning. All those little details which were new to me at that time like enemies dieing on a chair if you shoot them when they're sitting (Sounds silly...)
5. Fire Emblem Path of Radiance - Music and the story. Those are the two things that games lack these days but Fire Emblem is an exception. Also I have to mention character developement. (I've just beated the Black Knight on my second playthrough on turn 2 )