By "best" do you mean "most advanced" because personally i'm not a massive fan of polygons i much prefer sprites generally. But i gotta say Vagrant Story does look real sweet through PCSX ReARMed, WZ2100 is awesome too (though i'd love to see an updated PND soon) and yes Homeworld does look yummy but also dont overlook Classic Pandora stuff like Frogatto (lovely sprites) & Super Geometry Dust or Excellent Bifurcation. Each have their own awesome style, although its less 3Dish. i could go on for ages theres so many good games with excellent graphics styles on the Pandy. I almost forgot AAAA and Fish Fillets both brilliant graphics!!
Though now i'm trying to remember one i saw years ago, was puzzley platformish kinda thing where you played a tarball that could stick to stuff (its definitely NOT World of Goo) no clue what it was called.... if you can remember please let me know, think it used to be on OpenHandheld website