FFVI - Though I agree with Ender that it might not have as much detail as newer games, the fact that it has aged well is a testament to it's strong characters and good storyline.

Xenogears - It really should have been a novel or at least an animated series.

I can't say the same for Saga cause the internal politics really destroyed continuity. XSII went in a completely different direction under the new team and XSIII (though it was really good) spent most of it's time trying to fix the issues created by the change in the developement team.

Metal Gear series - Though, I must give special attention to MGS and MGS3 for both being incredibly well written and having a powerful human element in the game. Big Boss and Solid Snake will hopefully be remembered for being well written and well developed "human" characters and not just for cardboard boxes, snapping necks, and eating wildlife...

Ico - Solid proof you can write a compelling story and memorable characters, and no one has to actually say a word (or at least something you can understand).

Vagrant Story - MGS, SE style. Ashley is a compelling character, the narrative was strong, double crosses, mystery, political intrigue, and Sydney is one of the greatest villians ever written.

Final Fantasy Tactics - Even a shoddy translation could not hinder the compelling story and amazing cast this game had. Grand politics, church conspiracies, demons, betrayal, patricide, civil war, and bittersweet ending...