Hmmm....
Ken and Koichi (Digimon Zero Two and Frontier)
Seto Kaiba (Yugioh), Yuki (Gravitation) and Kai (Beyblade)
Haku (Spirited Away) and Prince Ashitaka (Princess Mononoke)
Fai (TRC) and Yuki (Fruits Basket)
Syaoran (CCS one) and Inuyasha (duh)
Ken and Koichi are the same, because they both got seduced by evil after having family probs, and spent the rest of their seasons making up for it. Seto, Yuki and Kai are the same because they act in the same way - cold and distant, but really aching for affection...they just had bad pasts that kinda scarred them.
Haku and Ashitaka are both kind, brave, and loyal to the point of extreme, and care for their opposite leading characters (Chihiro, Mononoke) deeply. They are also both drawn by Miyazaki, and look very similar.
Fai and Yuki both hide away under fake smiles because of their pasts, and Syaoran and Inuyasha, whilst gruff and a tiny bit arrogant on the surface, are big softies underneath, with hearts of gold.
Heh heh...is that enough? (sweatdrop)