The music and atmosphere of Fallabor and Verdanturf were the best and very soothing. They felt like magical places. I have a soft spot for Mossdeep as well - I have no idea why. Fortree was also cool, with the whole tree-house thing and the Kecleon event.
But the best cities have to be Sootopolis and Pacifidlog. Sootopolis was a very original city with a rich history, with the Groudon vs Kyogre event in Emerald being a definite plus. I always didn't understand how you could fly there, but that didn't bother me too much. Pacifidlog Town was another original location, with nice music (I think the theme is identical to Lilycove, though) and the way you could almost walk on the water was really nice. Getting to and from there without using Fly was always bothersome, though.