1. Suikoden II -- brilliant story, emotional characters, well-developed plot and world. This game just has it all, story-wise.

2. Final Fantasy Tactics -- There's an argument that this should be #1. A well-developed story of betrayal and tragedy, I could see this story being an actual book.

3. Lunar SSSC -- a more cliche plot than the top ones, but amazingly well-done with great characters and outstanding and often comedic dialogue.

4. Suikoden III -- there are some legitimate complaints with this game, but it can't be disputed that it told an epic story, and the three perspectives were done really well.

I can't think of what game I'd put #5 and I'm tired of thinking about it, so here's some honorable mentions: Final Fantasy VI, Suikoden I, Breath of Fire III