I'm always very coastal in my games; being British I only ever envision boarders being that of the sea and my play style reflects that.
Because of that Auckland and Nan Madol are always my go-to's.
Valletta I also love as if you have excess faith you can get new cities up to scratch quickly and you can buy those last levels of walls before you get Steel (for bonus Tourism). It's always nice to have either LaVenta, Granada or Armgh for the unique improvement so you can build it on un-improveable tiles such as tundra, snow and desert.
Buenos Aires, Brussels, Geneva, Kabul, Palenque, Stockholm and Zanzibar I like too.
I've yet to have a game with Babylon in it without it being conquered but I would image that it would be pretty nice too. All over city states are Ok, but not my preference.