Which games before the PS3-360-Wii generation had the best stories, do you think?

Kingdom Hearts 1/2, FFX and Tales of Symphonia off the top of my head.

The Final Fantasy games.

I really liked Kingdom Hearts... FFXII, Killzone

Alpha Centauri! A great space crash adventure game with many cultures philosophies.

I think it would have been more popular but some from the USA didn't like how they were portrayed.

For me, the standouts are Half Life 1 & 2, Shadow of the Colossus, Fatal Frame 2.

both zelda 64s, link to the past, ninja gaiden black, shenmue, resevil code veronica, halo combat evolved, and morrowind.

Planescape Torment
The Longest Journey, And Dreamfall.
Parasite Eve
Persona 3
Baulder's Gate II
Neverwinter Nights 2: Mask of the Betrayer (Might be this gen)

Final Fantasy and Deus Ex are my favorite RPG's, but I don't think their stories are necessarily the best, it's hard to describe but I find their aesthetics, and worlds extremely charming. But their stories often have things about them that bug me,  but ultimately don't stop me from enjoying (or in fact loving them more than games with better stories) because I find some of their worlds end up being more "fun" in the videogame medium.

There's also some games, Half Life, Zelda Series and Dragon Quest V for instance that tell their stories in an amazingly paced way and fit their respective games perfectly in a unique way. However, I don't find those games stories to have enough umph for best story.

Super Mario RPG
Eternal Darkness
RE1, 2, and Code Veronica
FFVII

easy MGS, FF and Kingdom “Mind Rape” Hearts