Cities can be named using:
- players names
-geographical situation (I usualy name in SP cities like Panama, Suez, Walvisbaai, Bunker Hill etc.)
-geopolitical situation (Hong Kong, Gibraltar, D-Day etc)
-Using the cities production: Science cities can be named after great inventors or scientists (Copernica etc)
-In large games (like this one) adding -Fort, -harbour etc will make it easy to see where to build vet-army and -navy.
Naming cities 'New Whatever' is not a good idea since you will not be able to distinguish the hometown of the unit.
Cities can well be renamed during the game, if this will make gameplay easier when running a large empire.
Captured cities should be renamed by changing just a few letters to reflect their incorporation in a different culture.