Phantom Menace. As people have pointed out it looks the best. I can't point out specifically why, but the backgrounds and the colors just make it look the best. And it has a great story with good political dialogue to boot. And the action is non-stop too. If you'll notice it's one action piece after another. From the escape of the Trade Federation, to the underwater ride, to the escape from Naboo, to the Podraces, to the war on Naboo, and finally the great lightsaber duel. Plus it was great to see everybody right from the beginning, from Obi-Wan to Palpatine. And of course there was Qui-Gon, which remains my favorite character.
As for AOTC and ROTS, they remain equally second, neither one greater nor worse than the other. Both good movies too.