Shadow of the Colossus and Okami like mentioned before.Also Braid, Morrowind, Oblivion, Vagrant Story, Ico (same team as SoTC), Final Fantasy VI and many others that I'm failing to mention. A game doesn't only have to have realistic graphics to be considerd a "beautiful" game.The style in the graphics, the music and just the way the game is made by creating a unique atmosphere makes a game truly "beautiful".

I would have to say Vagrant Story,especially the way it ended and how awesome that game is.But I don't think it will ever have a sequel due to poor sells (shame) and that it's been almost 10 years since that game without any new or even rumors of a sequel. A sequel to Braid or a spiritual successor of sorts would be nice to.