I don't think I've ever seen Okami featured in one of these lists. Just to be sure I looked up some of Polygon's and even in their Top 500, its not there, which is kinda depressing?
I'm not a fan of Zelda games - or most Nintendo games - but I do love when people take inspiration from them and make their own thing - Tchia, Darksiders, Oceanhorn, Tunic, and Ittle Dew all come to mind just as Zelda 'clones' - and I think there's no higher example of that than Okami, a game that takes its inspiration and surpasses it in every way. The graphics were at the time mindblowing(frankly, still are), with its japanese classic art style cel shading, the soundtrack is phenomenal and Amaterasu has an excellent mobility, zipping across battlefields or simply open areas with easy and fluidity. The paintbrush is a stellar tool, both to use in puzzles and in combat, and the game boasts a charming cast of characters and engaging story. Probably the saddest tidbit about it is that it was also Clover's farewell game, after its previous, unfairly lambasted, gem God Hand and two attempts at the beat'em up Viewtiful Joe series.
Nowadays the Zelda series has gotten a whole different kickstart with its open-world entries, burying these inspirations even further, but I still believe Okami easily stands atop most entries of that series, and on its own as well.