Best story/plot in a video game. Period. The 2nd disc may have got shafted, but it doesn't ruin my overall experience as a game. Even at a young age of 12 when this game came out, the way this game came about presenting itself really got me into games with a heavy plot/story.
2. Final Fantasy XII
IMO, the most unique and special Final Fantasy in the series. Excellent story, great battle system, best characters and most of all...no random battles.
3. Star Ocean: The Second Story
So the story is not so great in this gem, but the superb gameplay makes up for it. Item Creation allows up to thousands of possibilities for creating healing items, weapons, armor etc. The battle system's real-time engine is perfect for the PSone era and it keeps the action non-stop. Overall it's got the best replay value, allowing to replay the game as a 2nd character.
4. Super Mario RPG: Legend of the Seven Stars
You couldn't dream up a better story than this game offers...putting Mario and "the gang" in an epic adventure RPG style is probably the best idea since sliced bread. Somewhat difficult at times, the gameplay takes a turn-based approach using classic weapons and attacks from Mario's history. What many thought WOULDN'T be done WAS done when this masterpiece. This would have made the list at a higher spot if the game had been longer, as it can be beaten in roughly 20-25 hours.
5. Final Fantasy VIII
After the infamous Final Fantasy VII was released, Squaresoft had to come out with another 'banger'. Final Fantasy VIII was no stretch of the imagination but took the series another huge step forward with the 4-discs of great storytelling, unique upgrade system (Junctions), great FMV's...etc.