My games tend to take a long time, I only play 2-3 turns a day, so it usually takes me 2-3 months to finish a game. (I've always played huge worlds, so that doesn't help). No rush to finish a game, I just like to enjoy the journey.
Anyway, I try to name my cities something creative or relevant to its geography - it serves two main purposes: (1) it provides immersion and (2) it helps me located the cities if I've been away from the game for a while.
Some examples: (warning: some of these names may be corny & some probably would only make sense to a delusional mind like mine... you've been warned!

)
1. My capital city is usually named Macross City.
2. From there, my expanding circle of cities may be named alphabetically - so that the northern-most city of my empire could be something like "Arden Fair" and the southern-most city could be "Zentraedi"
3. Or I might use directions to indicate their general locations from the capital. Some city names could be "Northern Lights", "Eastridge", "Southern Cross", and "Westpoint"
4. Other cities might have names that quickly me clue in where they are at - such as "Cove", "Mountain View", "Half Moon Bay", "Rivermark", or "Dante's Peak."
5. Islands have names like "Midway", "Pearl Harbor", "Thermyscira", etc.
6. And then there are also other cities that are named for their significance or status - "Rivendell" is often my 2nd capital (i.e. Forbidden Palace), "Victoria" is the renamed capital of the first civ I conquered, or "Moonglow" is the city where I built the Great Lighthouse.
Other than cities, I also give unique names to Elite* units and Aircraft Carriers to keep track of them. My first aircraft carrier somehow always is named the SDF-01
Enterprise.
