My favorite towns of all time are Pacifidlog, Fortree, Lentimas, Resort Area (if it counts) and last but definetely not the least; Ecruteak. Why?
Pacifidlog: I mean really, who wouldn't like an epic little fishing village in the middle of the pokemon ocean?
Fortree: Dem treehouses... All you need to be impressed
Lentimas: A small town with a volcano next to it and ash falling from the sky? Oh boy.
Resort Area: Not sure if it's really a town, but I love it. A cool-looking resort place where you can have your own villa and fish up some level 90 Magikarps? Hell yeah!
Ecruteak: One of the coolest towns with beautiful landscape, beautiful music and cool pieces of the Japanese culture. Who wouldn't just simply love it?