Kanto: Probably Celadon or Cinnabar. Not too sure which one I prefer... :P
Johto: Probably Blackthorne, but Goldenrod is a close second. :D
Hoenn: What were they called again. XD Anyway, it would probably have to be Sootapolis, just because it's underwater. XD
Sinnoh: Snowpoint, just because I love snow. Though Sunyshore is pretty awesome too. :D
My overll favourite has to be Blackthorne City. Mainly for the nostalgia. XD Though it is a pretty cool city. :D