The MGS games really do consistently have the best boss battles. The flying colossi in Shadow of the Colossus were all fairly amazing, too.

I enjoyed most of the boss battles in Twilight Princess, though most don't seem to acknowledge them. They certainly riffed off of Shadow of the Colossus, but I think there was enough of a Zelda twist to keep them particularly interesting. The one that stands out the most to me was the dragon battle with the dual hookshots. I forget the particulars, but I do remember having to grapple between multiple areas to follow him up into the sky. It was very impressive to me.