Two things to consider about Kuja's sexuality:
a) his feminine looks are much like Sephiroth's; it's a style of anime called bishounen (or something like that).
b) although this hasn't really been discussed, he is clearly not gay. Pay attention to how he treats Garnet on disc 2 in Brahne's castle. He is very domineering over her, as if she belongs to him. Yes, this sounds stupid in text, but play through that bit and think of him as homosexual. It just doesn't fit. I'd call him 'flamboyant' and leave it at that.

He is one of my favorite villains, out of all of the Square games. Lavos was hardly sentinent, Ultimecia was hardly developed, and I didn't like Sephiroth (Eve from PE was pretty cool though . . . ). His motivation is fascinating. It appears at first to be simplistic and unimaginativly contrived, but it turns into something much more than that . . .

The Dark Messanger, though, while cool, is NOT the best final boss battle music. I would give that honor to either The Legendary Beast (Griever's) or The Extreme (Ultimecia's). Not OWA either.

(note: I'm a newb, can someone PM me and tell me how to get spoilers not to appear; all of the colors in the menu show up on the blue background, and I'm at a loss for how to proceed.)