Istanbul
Visit the main monuments around Sultanahmet Square on your first day. Topkapi Palace requires at least 4 hours, the Hagia Sophia 1.5 hours, the Blue Mosque 1 hour. Add the Underground Cisterns of Yerebatan (1 hour) if you have any energy left. Reserve the second day to explore the city. Visit the Grand Bazaar, the Egyptian Bazaar, the Kariye Church-Museum and the Archeological Museum. Climb the Galata Tower. Make a Bosphorus tour by boat. Walk Istiklal Avenue in the evening. On your third or fourth day make an excursion to the Prince's Islands for a bit of Turkey that hasn't left the 19th century.
North Aegean
Istanbul to Çanakkale is a boring drive of 4 hours. Take time to visit the surprisingly evocative Gallipoli Battlefiels. They deserve a good 3-hour detour. Troy, by contrast, is a disappointment. Assos is a lovely town: it has a very archaic upper village, a tiny harbor with some good restaurants, and beautifully clear sea. There are some pretty small hotels both inside the village and on the coast to either side, but none that offers much in terms of standards. You will find some excellent country hotels in the hill villages along the north coast of the Gulf of Edremit, notably in Yesilyurt, Adatepe and Çamlibel. The Island of Cunda, opposite Ayvalik and connected to it by a causeway, offers an attractive old town and some excellent seafood restaurants. It is worth a 3-hour detour. The ruins of Pergamum/Bergama are impressive enough on their own, but pale in comparison to those of Ephesus. You may skip them in good conscience and save time for Ephesus.
Ephesus and Around
Take a day to visit Ephesus and dependencies - Archeological area (2 hours), Museum (1 hour), St Johns Basilica (1 hour), Virgin Mary's House (1 hour). Second day: Visit Tire (Tuesday market a must), Birgi (Cakiraga Mansion, the prettiest 18th century house in the country), Bozdag (mountain lake) and Sardes. Third day: Visit the National Park for hiking and/or swimming. Visit Kusadasi for shopping or nightlife. Fourth day: Visit Aphrodisias and Pamukkale.
Driving Ephesus-Bodrum
Sirince to Bodrum is a 190-km drive. It can be done in 2.5 hours, or expanded into a full-day trip.
Reserve two hours for Priene and an hour for Didyma. Make a detour to Doganbey and Karine if you like getting well off the beaten path. Make a detour to the fabulously picturesque ruins of Heraclia on the far shore of Lake Bafa (2 hours). Check out the old bazaar quarter of Milas. Reserve time for the Tuesday Market of Milas.
Bodrum
Bodrum has a lively harbor area, a spectacular castle, some excellent restaurants and great nightlife. It is not a very small town anymore. You may stay in the town itself to be closer to things, or choose any one of a dozen coastal villages around the peninsula. Türkbükü is the fanciest (it pretends to be the Turkish St Tropez). Gümüslük has a lower-key, pleasant atmosphere and some nice fish restaurants. Don't miss the out-of-the-way hamlet of Karakaya near Gümüslük.
Southern Aegean
The coastline between Marmaris and Antalya requires a lot of leisure to explore properly. There are a lot of very nice towns, dozens of ancient ruins hidden in the mountains, some stupendous landscape and the best beaches of the whole Mediterranean. Our favorite towns are Dalyan, Selimiye-Bozburun, Kalkan, Kekova and Olympos-Çirali. Kekova is especially out of this world. For the most romantic ruins choose between Knidos, Kaya, Tlos, Myra, Olympos and Phaselis. Avoid the mammoth-hotel coast between Olympos and Antalya.