Well, I'm mainly comparing Soul Calibur 1 with Soul Calibur 2(though it happens for pc to dc as well, house of the dead 2 on dc versus house of the dead 2 on pc, or the phantasy star games... and those are the exact same games but they look different, dreamcast is slightly sharper), I guess a port of a psone game would have a simpler color scheme than a game made from the ground up for next gen systems. The difference does depend on the size of the screen used though, when on larger screens soul calibur 1 looks much sharper, but when on much smaller screens soul calibur 1 looks only slightly sharper.
I believe the gamecube version of soul calibur 2 is supposed to lack mip mapping or something though.
BTW, why should all 640x480 images look the same? N64, PSX, and PS2 definetely don't have the same output quality as other systems. Even nvidia and ati cards on pc don't have the same output quality.