Ok, digging around here, I think I made a big mistake here.
In your science city, you want commerce. So, build cottages first I assume; not farms, right? I was erroneously thinking commerce is money and science would have nothing to do with commerce (and be from the old concept of "trade"). That was old school thinking.
So a Science and Money city would need lots of commerce, but one would have the money improvements (banks, markets) and the other would have the city improvements (library, universities). That is essentially the only difference. And coastline is also a great source of commerce it seems?
So this begs a new question: What do you do early on in--for example--in your science city when there really aren't a lot of science improvements to build. You build you library, and then??? start stock piling troops?
It seems no one here has any use for religious buildings, happy building, health buildings, or culture buildings?
I would assume you would need a courthouse, police station and a granary in each city? (to go along with your specialized buildings...)
Yes, commerce cities are for science. Unless you are running a specialist economy the main thing for these are cottages, tons and tons of cottages. Coast isn't bad but they just can't compare the longterm rewards cottage spamming can create.
The main thing you want for a cottage spam city is as much green grasslands as possible, as its two food makes for a great location. Floodplains work even better, but are harder to come by. Avoid too many hills or plains. Also keep in mind that under jungles are usually
lots of fertile fields just waiting to be cottaged if you can summon the man power to chop them down. Spaces next to rivers are the best, as they provide an extra +1 commerce bonus.
In the early stages of the cottage spam however, building farms may be best. You want to get your city as large as possible as fast as possible (until it hits the health/happy cap). Having a dozen cottages won't do you any good if you can only work two of them. Once your city has grown, you can cottage over your farms.
And while this isn't always possible,
ideally your actual gold city will be a holy city with a nice, well-spread religion. If you can, found and spread it (a reasonable amount) or just capture an enemy holy city. Get the holy building built, throw in a market, grocer and bank... run some merchant specialists and you're good. If the religion is large enough, you can support your entire economy on almost a single city, allowing you to set the science slider real high. Owning multiple holy cities is even better, if you can get the great prophets.
As for your other questions, yes, pretty much every city needs a granary as soon as possible. Courthouse too, unless its your capital (or right near it). Jails aren't exactly as vital... put them in your major cities, as those will suffer the most from war weariness. And these are all things to build after your library is done. And don't forget Monastaries also increase science! Get a bunch of religions in the city and you can build a lot of those.
As for the other buildings, there is certainly a use for them. It's just situational, see if your city needs them. A city should always be generating
some culture so at least one culture building is a must if no religion is present (libraries count) and if it's directly competing with enemy culture, you'll want as much as possible. As for all the health/happy buildings, just look at you're cities limit. If your city has plenty of health but is limited by unhappiness, forget the aqueduct and build a colloseum or temple. Grocers and markets are pretty great at adding these if you have the resources.
I tried a new game yesterday... (Well two actually, but I won't discuss the first one--it was bad). Anyhow, on my next attempt, I tried to focus on specializing cities. The only city "types" I was specializing on was Science and Production. Re-reading the above, it looks like I need a Commerce city as well. I assume one does not need a food city but food should be balanced in with the others? I don't really need a "Great People" city.
So, I decided with my strategy, I was thinking Memhed might be a great fit for me. In this game, I did something I have never done with Civ 4. I did not automate the settlers. I assume this was a good move? I learned alot about the resources because I never needed to concern myself with this before.
"Food cities" are actually "specialist cities", which also are great people farms. They can be very useful but somewhat situational, the easiest way to do it if you have like four good food resources nearby, such as a seafood capital. What you basically do is work the food tiles to get the city to its happy/health cap and then stop working as many tiles as you can (without starving the city) and turn them into specialists. Farm everything you can, mine hills for occassional production.
Scientists are typically the best. During this time, the city's production will be pretty low, but you can just switch off the specialists at will when it has something important to build, and then switch them back when you're done. Caste system and representation work well with this. All the specialists help generate a lot of great people points, who are useful!
Because of the micromanaging this requires, it's probably best you leave it alone until you get a better handle on the game and just stick to cottage and production cities. While helpful, it isn't vital.
Also the less automating you do the better,
expecially with settlers.
There is alot of possible answers for this one.
