Itinerary to visit Istanbul

You have to visit below places (ordered by importance/ must do)
1) There are many types of Bosphorus Ferry tours. http://www.turkeytravelplanner.com/go/Istanbul/Sights/Bosphorus/BosphorusCruise.html

2) These places are close to each other

Kapali Çarşisi (Covered or Grand Bazaar) http://kapalicarsi.com.tr/

Misir Çarşisi (Egyptian or Spice Market) http://www.istanbul-travel.net/egyptian-spice-bazaar.html

3) These places are close to each other

Haghia Sophia http://www.istanbul-travel.net/hagia-sophia-church.html
Topkapi Palace http://www.360tr.com/topkapi/index.htm
Sultanahmet Camii (Blue Mosque) http://www.istanbul-travel.net/the-blue-mosque.html
Yerebatan Sarayi (Basilica Cistern) http://www.istanbul-travel.net/basilica-cistern.html
Mevlevi Monastery http://www.istanbul-travel.net/mevlevi-monastery.html

4) Istiklal Street - Taxim http://www.istanbul-travel.net/istiklal-street.html

5) DolmaBahce Palace http://www.istanbul-travel.net/dolmabahce-palace.html

6) Istanbul islands (Princes' Islands) http://www.turkeytravelplanner.com/go/Istanbul/Sights/adalar/

Another list, you may find a few extra places in it.
If you go to Ortaköy, you have to eat “Kumpir” there. It is very popular.
There you can also have a tea(and eat simit http://en.wikipedia.org/wiki/Simit ) next to bosphorous and buy things from small shops.
If you like sweets, I would suggest buying baklava and other things from Gulluoglu, or MADO.
more:
Beyoglu (Pera): Istanbul's real centre now is the Grand Rue de Pera (Istiklal Caddesi). Nice restaurants and shops. Crowded.

• In the Sultanahmet Square :

• Istanbul Archaeology Museums

• Grand Bazar

• Spice Bazar

• Galata Tower: cross the Golden Horn Bridge and give a coffee break at Karaköy before heading to Tünel and going up the Galata Tower to watch the splendid view of Istanbul.

• Dolmabahce Palace

• OrtaKöy

• Bagdat Caddesi (Bagdat Street): the Anatolian side.

• • Istanbul hamams

The Museum Pass Istanbul is a museum entrance card that allows entrance to Istanbul’s twelve must-see museums, without having to endure the long queues. The 85 TL Museum Pass is valid for 72 hours (3 days) and the 115 TL Museum Pass for 120 hours (5 days) from the first museum visit.

The Museum Pass Istanbul gives easy access to:
Hagia Sophia Museum
Topkapi Palace Museum and Harem Apartments
Istanbul Archaeological Museums
The Museum of Turkish and Islamic Arts
Museum for the History of Science and Technology in Islam
Istanbul Mosaic Museum
Hagia Irene Museum
Chora Museum
Rumeli Hisar Museum
Yildiz Palace Museum
Galata Mevlevi House Museum
Istanbul Fethiye Museum (Pammakaristos)
You can save quite a bit of money with the Museum Pass compared to buying separate tickets for each museum. Recently the individual ticket prices have increased, so the Museum Pass is more beneficial than ever. The card is also crucial to anyone trying to save time. In the busy season for museums, the queues can be up to two hours long. Museum Pass Istanbul allows you to enter each of the twelve museums in only 30 seconds.
Museum Pass Istanbul gives additional discounts from 10% to 30% at elite private museums, more than twenty arts and entertainment venues, museum shops and GES Shops. You can purchase Museum Pass Istanbul from the ticket gates at Topkapi Palace Museum, Hagia Sophia Museum, Chora Museum, Istanbul Archaeological Museums, http://www.muze.gov.tr and Mobile Sales Stations. The two types of Museum Pass are also available at the concierge desk of the many hotels around the city, listed here. However, the sale of the Museum Pass at hotels is under discretion of the hotel concierge and reception.