Not gonna open the can of worms of trying to define "beautiful", but I will say this:
Cat Shit One is the best looking CGI I've seen in anime.
Princess Nine has some of the most beautiful music in anime that isn't composed by Yokko Kano. Instead, I'll have to tip the hat to Masamichi Amano and the Warsaw Philharmonic Orchestra.
Can't really decide on the most beautiful hand drawn anime. Just way too many to choose from throughout the 80s and 90s.
And, the most beautiful anime in the totally ambiguous, undefined, opinionated way:
Wolf's Rain.