Long weekend in Istanbul

There's a lovely small mosque, Rustem Pasa, next to the Spice Market. I very much liked the Mosque of Suleyman the Magnificent. I saw them both on the RS Old Town Back Streets Walk. Did you visit the Underground Cistern?

The Spice Market is super-crowded on Sundays, when the Grand Bazaar is closed.

If you haven't already, be sure to go to the neighborhood of Kadıköy, on the Asian side. You take a boat there (part of the regular Istanbul mass transit system and costs the same as a bus) which gives you great views, and the area, while hardly undiscovered by tourists, is very interesting.

If you didn't venture there last time then you should also give some time to exploring the Golden Horn.This is a very ancient district of the city comprising of Fatih,Balat,Fener and the Holy village of Eyup.You can go by bus but the nicest (and most scenic)is to take the ferry at Eminönü.Look for the Haliç Line,this is the Golden Horn in Turkish.
This are is rich in Byzantine/Christian and Jewish history as well as Islamic.In addition on the north bank is the wonderful Rahmi Koç Museum,Miniaturk,Sokollu Mosque complex and the lovely Aynalıkavak Köşk.At Eyup you can take the teleferik up to Pierre Loti cafe for wonderful city views.
Earlier someone mentioned the 1453 Panorama Museum;close by there is the Mimar Sinan creation Mihrimar Sultan Mosque also worth visiting.

I would also second the idea of a visit to Kadıköy on the Asian side for a different aspect of the city and,if you still have time,take a bus or ferry up to the village of Sarıyer to the north of the city centre.Nice for a fresh fish lunch on the waterfront but also chance to visit the excellent Sadberk Hanım Museum which is often overlooked by visitors.

What about the Mosaic Museum and Church of the Saints Sergius and Bacchus near the Arasta Bazaar (also worth going to - much smaller and more laid back than Grand Bazaar)? There are just walking distance away.
http://www.tripadvisor.com/Attraction_Review-g293974-d307885-Reviews-Mosaic_Museum-Istanbul.html
http://www.tripadvisor.com/Attraction_Review-g293974-d307883-Reviews-Kucuk_Ayasofya_Camii_Church_of_the_Saints_Sergius_and_Bacchus-Istanbul.html
http://www.arastabazaar.com/

I also really enjoyed Istanbul Modern Museum (on the Bosphorus, but closest tram stop is Tophane), taking the ferry up the Golden Horn (Eyup is really interesting), going to Kadikoy (try to find their little market stalls) and Uskudar on the Asia side, and visiting Dolmabahçe Palace (it's best to get there early as it fills up - it is a guided tour and absolutely amazing space). I have not been there, but I'd really like to go to the Sakip Sabanci Museum - also along the Bosphorus (north) in a beautiful location. Any trip involving a ferry on the Bosphorus or Golden Horn was a total highlight for me - you can just take a local ferry, no need to pay a lot for a tourist one. To me, that was the highest value for the price and I would do it again on every trip.

Personally, I loved strolling along the ocean front and then up and into Gulhane Park. Per chance came upon young runners competing in a foot race. Much fun watching the competition. also loved the out of the way restaurant I found up a steep flight of stairs in the Grand Bazzar. Could I find it again? Probably not but I do recall that I'd been listening to the gold buyers arguing and while walking away from the posturing saw a small sign saying restaurant with an arrow pointing up steep stairs. BEST climb ever as I still dream of the superb lentil soup that I enjoyed in the small hidden restaurant. Do you play backgammon? Might drop in a cafe or team to see if you can play a game? Lastly, I loved cruising to the Asian side and exploring there.

Thank you for all of your replies. I did spend three days earlier in June in that wonderful city. This is what I did.
I had trouble with my debit card (I won't tell you WHICH bank). When I arrived at my hotel my reservation had been cancelled because of my debit card. I was offered a room at a hotel much further out than Sultanament, which I refused. I did accept a room in a hotel which was off the Tram Line. "Go up the tram line until you get to Burger Kingand then go straight down. That was good advice but no one knew there were 2 Burger Kings.
My first visit is always to Mustafa and Hagberti at Troy Rug, number 39 in the Arasta Bazaar. Then, because it was, after all, Ramadan I floated up to all the lovely traditional crafts sold in the stalls in the Hippodrome. My favorite purchase was a "horn" comb. I also bought a lovely red-felted chNge purse.
As I said before, I had trouble with my debit card and spent much effort trying to get my information FAXED to the U.S.A. People in Istanbul do not know what fax is and most do not use printers. The kindly people at the front desk at the Four Seasons let me use a computer and the printer in their.business center. Wonderful, but my U.S.A company couldn't accept the fax.
In the midst of all this, I couldn't sleep well. One morning I left the hotel at 5:30 A.M. And headed back to Sultanamet. Where rock bands had been playing the night before, there were now spotless sidewalks and parks. I took the best photographs of my trip with the morning light beaming on the Blue Mosgue and Aya Sophia, also a huge "bowl" with oranges and cut-open pomegranates.
A friend squired me through the ancient Byzantine section. We visited a large mosque on the cusp of a hill, had "toast" at a little corner market and were entertained and entertained three beautiful, clean Syrian children. The two of us where drinking our Aryan (yogurt) when the littlest boy took our covered straws and later played them like a horn with the wrappers still on.
We did walk through a water pipe place of of the Tram Line.we stopped and had a
Mostly I just walked around and enjoyed Istanbul, visiting and eating on board a fish boat, having dinner at a seafood restaurant under Galata bridge.
Pam from Bath.