i have been to a few:
the florida aquarium in tampa
the key west public aquarium
the national aquarium in dc
the baltimore aquarium
my fav would be the baltimore aquarium. you start at the ground level and sprial you way up to the top, then you take the inside sprial down the center which is the shark/larger pelegic fish exhibit
the key west aquarium is cool because it is so old, its all open air. not very big but still really neat.
i have not made it to the monteray bay aquarium, but its on mylist of things to do.