I'll echo the mention of SotC and add Ico:
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It's hard to top these games, but my unequivocable #1 due to its sheer breadth and depth of beauty is still Valkyrie Profile: Silmeria--
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In some cases, if I didn't know better, I'd say Silmeria looked like a PS3 game. Not just because it pushed the limits of the hardware technically, but Square/Tri-Ace just hit a gd aesthetic grand-slam with this game. It's just plain gorgeous, and is one of the few games from the era that has aged well (remarkably so, IMO). Perhaps this is because--like Ico and SotC--the devs chose a stylized art direction over attempting photo-realism (on the PS2, LMAO were we ever that young??).
Shit on that note, I gotta mention the obvious as well:
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FFX, another grand-slam of technical wizardry and human imagination.