<< man, if you've got component outs and component in's, it would be a shame not use them. and yes, there are subtle differences. not as big as the difference between regular input and s-video, but still differences. >>
Actually each has their advantages, s-video has better white/black(contrast) reproduction but inferior/mediocre color., component on the other hand has superior color reproduction but inferior white/black seperation. S-video can actually look better in certain high contrast scenes with simple background(not color rich).