Looks like I'm a bit late to this topic as the mudslinging is already underway
I'll give my answers anyway and thank you Thunderfall for the great thread!!
1. City in the long run: I see that I am not alone in choosing D. It seems that just about every square other than the ocean ones will yield production and (eventually) a fair amount of food. Also, as early as size two you can have 6 food, 5 shields and I believe 2 or 3 trade arrows by using the two specials. This will help greatly in the beginning. A quick road and an irrigation or two will put it over the top.
2. City in multiplayer: I have never played multi, but I can assume that coastal cities can be vulnerable. Since they are all coastal, my first choice would again be D for the reasons above. F would also be OK, and the swamps could even provide for some added defense if necessary.
3. City for Science: Things I look for for a science city are -
1. Trade specials (silk, gold, etc.)
2. Plenty of water (ocean or river)
3. Growth potential
4. SOME production - though this isn't paramount.
I still like site D with all of those in mind. There are 10 or 11 water squares in total with ocean and river, and while the specials are not trade specials, they will help both growth and production. Growth for more people working and eventually scientists and production for quicker library/university/wonder building, etc.
Keep in mind that all of the cities save one were built in areas that had to take into account neighbors and watch for overlapping - so don't judge too harshly.
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Diplomacy - the art of
saying "Good Doggie"
until you can find a rock