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I'd have to say Celadon, don't remember why, Saffron, because of the train, and Lavender because it was small compact, and had ghosts, even though i hate 'em.
Goldenrod City because its so huge and big and theres so much things there liek the massive mart, train, radio tower and the national park..... best city in the 2nd generation!
In Kanto, my favourite town/city is probably Saffron City... because it has one of the most fun "dungeons" in the game - Silph Co.. I always look forward to that part of the game. My second-favourite town/city is Cinnabar Island... for about the same reasons. I enjoy playing through the Pokemon Mansion almost as much as Silph Co.
In Johto, it would have to be Mahogany Town. For some odd reason, my starter (Cyndaquil) always evolves into its final form down in the Team Rocket hideout. It's like some kind of tradition or something...
I love Cerulean City because being that Misty lives there, it reminds me of the original Pokemon series episodes I started watching 10 years ago. Lavendar Town(the ghost city?) is neat too, because it is kind of hazy and strange.
Olivine is pretty neat for the same reason as was mentioned above...the lighthouse. I also like Mahogany Town because it seems quaint and peaceful.
Saffron city, that one city with the grass gym, pallet town, goldenrod city, and blackthorn city are all my most memorized cities. i especially remember saffron because its like, the center of kanto. the grass gym city because it was the first town that had the super mart. pallet town because its the starting town, goldenrod because i could never beat the gym leader there, and because of the radio tower and the big mart, and blackthorn because it had that awesome cave above the gym.