My best city experiences in the empire building genre come from Call to Power.
Call to Power was the wargamer's Civilization. A game where trade monopoly and a heavy production cities were the heart of your war machine.
Early in the game you would come across giant annoying mountain ranges that you horses had to go around. Many many turns later however, these giant mountain ranges would become sprawling mecha's of production as you heavy mined every single one of them.
So I was playing this one multiplayer game against 1 other guy. We had been playing this game for weeks and weeks. Deep into the modern age and beyond.
He has 1 continent and I have the other. According to the charts, I am out ahead of him in production and money by a decent margin.
We both know war is coming soon, so I start filling my cities with the biggest toughest warmachines that I could build. Eventually I filled each city with 4 of these before he launches his attack. I had well over 80 cities, and within 20 turns I had lost 15 of them to his invasion.
He was pushing deep into my empire, but luckily, his push bottlenecked at 1 single city that was a 1 tile archipeligo leading to the rest of my empire and some gigantic mountain ranges where I was popping out tanks 1 a turn in all the cities. He even had 2 fleets bombarding this little city.
I held him off at that 1 vitally strategic city, and manage to leverage my heavier production against him pushing him back out of my nation. Recaptured all my cities and used the underwater tunnels he built to get to me against him.
A 3 week struggle ended with 1 little city holding ground against all his armies and fleets.
So, that city will forever be in my mind. As well as all the rest of my heavy production mechas from Call to Power.
My favorite city of all time from RPG's would have to be Borealis from Anarchy Online.
I don't really remember how I even found the place. Just a noob wandering around getting lost. All I do know is that as soon as I had found it, the throngs of people all over the place stood out as different from all the other vast cities in that game.
This was the place that everyone gathered to trade and socialize. This city also happened to be neutral which meant that both factions, Omni-Tek and Clan could hang out in one location, because most other major cities on the planet had them at each other's throats.
So you would walk into this living city, quite unlike the masses of people you might see in a city in games like Lineage, CoH, or FF11. People in this city had their place. If I wanted to sit and chat with any given Neut guild I knew right where to find them. Some of their members would invariably be found there and more often than not you could watch them actually log in and out in their corner of town.
You could wander around and find all kinds of groups hanging out in various parts of that small town, and it was always the same, and yet different at the same time.
It was a true living city. Familiar yet without the boredom you get from your average small MMO/RPG town.
It was a major hub of activity, whether you just want to sit in a group and chat, or trade, or grab someone to take out into the shadowlands.
I found out later that there were a couple other similar hangouts in various places on the planet, but this was Neut territory and it became home.