Our cruise ship will be stopping at Istanbul 2 days (over night). How does one get from the cruise ship terminal to the main part of the city?
What are the "must see" sights (besides Hagia Sofia)? What neighborhoods/areas are OK for tourists but not too touristy? I want to eat some real Turkish food, any recommendations?

You want to go to the old city. (Don't know how to get to the from the port, but would imagine a taxi.) Right next to Hagia Sophia is the Blue Mosque, one of the most beautiful spaces I've ever seen. You can also wander from there to the market/bazaar. You should also walk over the Galatea Bridge, across the Bosphorus, from the old city to the new city (or vice versa)

Depending on how much time you have, you might want to visit some other mosques. My favorites were Rushten Pasha (for the tiles) or Suleymaniye (the big one). Also fun is walking down I. Cadessi, the main shopping street in the new city. And if you have time, you could take the ferry over to Asia (all the ferries leave near the Galatea Bridge). Topkapi is also pretty amazing, if you have the time for it; there is a great little restaurant for lunch overlooking the water called Konyali.

There is so much great food in Istanbul. We most enjoyed the street food, especially the fish sandwiches the men were selling off the boats near the Galatea. The restaurants I remember from my visit (but it was 2002, so no guarantees they are still there or still good are)

Rami (sort of French influenced Turkish, but amazing. We went there twice)
Cennet (not very posh, no liquor, but they do these great gozlome--sort of Turkish crepe--and you watch them make them)
Yesil Ev (also good, but a bit fancy)

There's also Kumpaki Square, the entrance to a restaurant street where the waiters "invite" you in. (Hard to choose which one, but according to my journal the one we went into was called "Aprhodit")

Istanbul is amazing. We spent 10 days there and didn't see everything we wanted to.

We love Istanbul, one of the things Rob enjoyed the most and wants to repeat when we return this fall is to go and hear/see the Mehter, or Janissary, Band perform at Dolmabahce Palace. They perform on Tuesday afternoons during the summer in front of the main gates, and at the Military Museum the other days of the week.
It really is a sight and sound treat for the senses.

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Suleymaniye

I'd say it's a must-see. The glass windows are amazing! I second Constance's appraisal of the Blue Mosque. Topkapi Palace (museum) is also in the vicinity. From the Turkish tourism website:

"Sultanahmet: Many places of tourist interest are concentrated in Sultanahmet, heart of the Imperial Centre of the Ottoman Empire. The most important places in this area, all of which are described in detail in the “Places of Interest” section, are Topkapi Palace, Aya Sofia, Sultan Ahmet Camii (the Blue Mosque), the Hippodrome, Kapali Carsi (Covered Market), Yerebatan Sarnici and the Museum of Islamic Art."

The website address is: http://www.ee.bilkent.edu.tr/~history/topkapi.html

Blue Mosque, Topkapi Museum, Hagia Sofia, Bazaar. All touristy but all fantastic.

Basiktas (not sure of the spelling... pronounced ba SHICK tas)- the area immediately south of the Sultan Bridge on the water...lots of fish restaurants and outdoor market in the evenings.

A boat tour of the Bosphorus....you will get the most fabulous views of Istanbul.

Di

There were two truly wonderful shows on the History Channel this week on Istanbul and the underground. Also the Roman connection. If you get a chance to watch these shows it will be worth it as they show a great cross section.

Also something to do that we enjoyed was the 'Basilica Cistern'. (Discussed in the History Chan. show)

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Originally posted by Diana Strinati Baur:
Blue Mosque, Topkapi Museum, Hagia Sofia, Bazaar. All touristy but all fantastic.

Yes, that's why they're "touristy" :-)

Incredible sights all packed into one fairly tight space too!

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A boat tour of the Bosphorus....you will get the most fabulous views of Istanbul.

And it costs only $3.00 US for the 6-hour round trip. This cruise is in one of my photo sets of the Turkey trip though it was, after 25 days, the ONE overcast day we had when in Turkey. The water would have been so beautiful if the sun peeked out every now and then but it is such a great ride and bargain. Seeing the part of Turkey in Asia and the portion in Europe at the same time is one of the features of that ride.

http://www.pbase.com/andrys/turkey

Oh, since you won't have much time, you might do what we did, as we had only 2 days there, at the end of our 26 days. The BUS that takes you all over that large sprawling and interesting city. It costs very little, maybe a few $ but you can get on and off it all day. And the top deck has no covering so that was a GREAT ride.