Personally I love In The Evening of the Moonlit Night in Studio 4C's Digital Juice compilation [download]. It's rather beautiful IMHO and is remarkably detailed. Definitely worth a watch for anyone interested on how an AMV where the animation is solely for the vid could look.
I think there's a Ghibli and a Gainax vid too which are fairly popular. Anyone wanna provide links?
I also quite like the amv that is the last third of the Utena film too
