It's a three-way tie between Ecruteak City, Nimbasa City, and Snowbelle City:
Ecruteak is the first city I really liked in the main Pokemon games; after all, it's home to my favorite Gym Leader (Morty <3), the legendary cats/beasts, Ho-oh and the Tin/Bell Tower, which was fun climbing through! I also really love the Dance Theater's music, and I like the Kimono Girls, especially considering that they each use one of the pre-Gen. IV/VI Eeveelutions. I was really glad when HGSS made Ecruteak's music unique from Cianwood's, and that it turned out very beautiful.
Nimbasa I love for its festive music and things to do. Love going to the stadiums and on the Ferris wheel, and Elesa's gym in BW is one of my all-time fave gyms due to the roller coasters and Trainer classes found there. (Rich Boys/Ladies + Amulet Coin = lots of money, whoooo!)
Snowbelle I mostly love for its architecture, geographic location, and music; the third is my fave of all the cities'. I also love the types of clothing sold there, though it isn't my fave place to get clothing. I really wish they added more to it so I could've stayed longer, though I do often go there when Wonder Trading, Super Training, or playing with my Pokemon on Amie!