Horteka was the green South American-themed city in the trees. I don't remember if it was through the vortex or not; that may have been Yafutoma. (Speaking of which, I liked the way some of the houses there had streams running through them.)

A good way to tackle this would be to come up with a list of 'specials' that can be applied to any city in the game.

Each special is completely unique, and once it is tied to a city, that city is 'special' in that manner for the rest of the game.

1) Thematically tie specials to the various races/backstory elements

This instantly gives specials a leg up over generic upgrades, because they ARE unique, and (if well written), will become memorable and instantly recognizable

This also has the benefit of creating a culture of communication on forums, as you can complain about the cities your opponent has, and gush about the ones you have, and everyone knows exactly what you are talking about.

2) Allow specials to give interesting abilities, upgrades, or perks that are NOT of the +5% production variety

Instead, have city specials that grant unique abilities, eg

Cast a unique and powerful spell X every Y turns for Z cost

Have activated abilities that could temporarily enhance some aspect of your empire, economic, military, or magical

Recruit a special unt

Recruit a special hero

Purchase unique artifacts

*Greatly* enhance some aspect of your empire around that city (again, not a +5% production bonus) - double unit production, greatly strengthen or weaken one school of magic, etc. Some might even be slightly double-edged, or at least, unique enough in their application of modifiers to force a slightly different playstyle around them for development or combat

3) Specials could have a distinct visual appearance, making them recognizable not just in the detailed info for a city, but at a glance from the map

4) Specials could have distinct audio cues - musical tunes, sound effects that can be heard while near them on the map

5) Specials could have stories tied to them, visible through info on the city

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Specials could be placed on cities automatically, some could be developed or built, some could be acquired through choice or chance, some could be acquired through spells (or perhaps inflicted?)

The keys points here though are: Unique, recognizable, and interesting.

   Most cities are made of people moving and doing different things.  If there were real-time animations for  shopworkers, smiths, Bard or 2 singing songs, birds flying nearby, etc.  Also, the animations should not remain static.  They should move around, go into buildings, go to their housing at night for sleep, sweep the stable, etc.  They could call out to each other once in a while, "Greetings, stranger.", "I am Mystic X; have you seen my pet Slithereatemous?  He's been bad today, having run off an eaten a few peasants!"  "No?  Well if you see him, can you please avoid his stomache and bring me this news?"  "Thank you, good day."  Colored smoke billows out as Mystic X voice and body fades away.  I would also randomize the appearance of different city characters/inhabitants so that each game you would generally get completely different population and voice characterizations.  Maybe if you play the game a hundred times in a row you might get a few of the same faces/characterizations.

Baldur's Gate.

Of Baldur's Gate.

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.  

What would be really neat, if doable, would be to be recognized by the Permanent Residents of at least your first settlement that has grown with you over time.

Considering you are the one responsilble for ALL things, being the SOVERIEGN and all, a baker may offer a loaf of bread, kids would swarm around seeking whatever copper you might drop (it is something you have done for years, a way to ensure a set level of wealth in the town as it overcomes it's early growing pains and develops into a full fledged Major Cosmopolitan City of your Realm...

It would be very cool to be able to go into many of the building who should serve a function.

The Library, The Town Hall, The Jail, The Barracks and converse with the proprietors of said buildings.

Ambient sounds, as realistic as possible is also a very critical item for any Hamlet/Town/City to distingiush it. (as already noted above)

Lol...sounds like the old Don that de niro stiches up in Godfather 2.