The famous Virgin Megastore at City Stars in Madinet Nasr is an important place to find many books from children's to scientific, art, literature and personal development books. They get the latest released editions of both Arabic and English books. Offers are available during some seasons. Virgin also sells music, DVDs, electronics, etc.
Go to Virgin if you are looking for a new book or edition.
Can also be found at City Stars mall (first floor). They have a wide variety of Arabic and English books. Some people think their prices are better than Virgin but I never really compared, I go there directly if I'm looking for books published by them.
American University in Cairo (AUC) Bookstore
Address: 113 Kasr El-Aini St., in Hill House on the Main Campus, Downtown. Telephone: +20-2357-5377 / 1.
"Alef" is the first letter of th eArabic alphabet. They have many nice offers and events. Can also be found at City Stars, Zamalek (2 Taha Hussien St., Zamalek) and other locations, check the website for their addresses.
Found in Talaat Harb, Downtown or El-Batal Ahmed Abdel Aziz, Mohandeseen.
Another prominent bookstore in Cairo. Has a few branches, check the website for addresses.
Soor el Ozbakeya
This is a very special place in Cairo where you can find all types of Arabic and non-Arabic books for amazing prices. You can find used books in very good condition, rare books, old books, academic textbooks, everything! It is a wide area where many kiosks sell hundreds and hundreds of books. To get there, use the underground (metro) towards El Ataba station.
Check this link for a list of Bookstores and their addresses.