Well... Some more suggestions :)
At first it's tourism. There may appear some foreigners in a city. They don't produce shields/food and you can't make them be labours, but they are in a city and make some commerce points(and, perhaps culture and victory points). Of course, they wouldn't appear in a miserable civ or city... They'll appear only in "great" cities where are about 2 or 3 Wonders or warm coastal waters. But they'll produce pollution :D ...
Or they(tourists) may appear in a city that have casino... This buildings may produce commerce and corruption.
Religions... Well it's the most difficult and the most arguefull part of my ideas. When you achieve politheism/monotheism you can choose religion type(the same as government type). Each of them will have some advantages... For example(I don't mean these adv. will be in real) islam makes units cheaper, catholic give +1 culture to every city, protestant will give commerce, orthodox christian will make workers work faster.
City specialization, or perhaps "colony" specialization. I mean when you command your worker/settler to build city/colony(perhaps cities are better) you can choose between military, where you can build only military units - no workers, settlers, buildings or wonders and they gain +1 from every spot that have a shield and units are cheaper; scientific cities - no units, only sci-buildings and sci-wonders(Newton's Univercity); food cities - they make only food(no shields => no units) and feed other cities ; standart cities - as usual, everything.
Food trading... This means that if a city has enough food and there's a shortrage in some cities of your empire the "lucky" city will "share" their food with "unlucky".

I like the idea of food sharing but it should only become available once you have discovered refridgeration or similar tech otherwise you wouldnt be able to realistically share food over a large area

Religions will be present in cIV, from the rumormill info. What isn't known is if you get to choose which religion or influence it in anyway. I think it would be cool if you could declare a national religion (bonuses in cities dominated by that type; perhaps rioting in cities that were dominated by another religion?).

A more comprehensive trade/tourism model would be great. It's kind of abstracted right now with Wonders producing 'tourism' money after (i think) 1,000 years.

I'm a big proponent of SMAC-style gov't, and being able to enact 'policies' (independent of gov't). Maybe you could discover "Marketing" and enact "promote tourism" to get a bonus to commerce, but also increased pollution. Or after Economics is discovered, you could enter into "Free Trade" agreements between one or multiple civs, which would add commerce (and pollution) to all cities on the trade routes...

...and speaking of trade routes, wouldn't it be cool if you could designate major trading routes? Or perhaps see the flow of trade in your borders (perhaps a map overlay) so you could see the trade routes? Imagine having that information. You could have a unit 'attack' the trade route and steal some gold (or goods, or something) or you could destroy a vital road and disrupt trade between two civs.

More functionality on that would make the game a lot more enjoyable (and realistic).

Trading food is also a good idea. I don't remember who said it, but a good idea put out there was the effective range of food trading would be dependent on techs you have, and could only be done by connected cities. Hopefully something like that will make it into cIV.

I don't fully agree with you on colony/city specializations. I think perhaps when you settle a new city, it should have a 'special' designation that lasts until, say, it becomes level 4, at which time it becomes a regular city (even if population lowers below level 4). Then you could have: Fort cities (military bonuses), Resource colonies (commerce bonuses, must be built ON a resource), Culture cities (bonus to build culture improvements, for those nasty culture wars), and the like.