You're sure to encounter a sensory overload of city tours and out-of-town excursions once you arrive in Istanbul, because fly-by-night tour operating seems to be a highly lucrative pastime. A popular organized day trip is the cruise up the Bosphorus, which can be taken as a half-day or full-day tour. This usually includes a quick stop at the Egyptian Spice Market and a visit to the Rumeli Hisari. But read the fine print, because if business is slow, they'll put you on the public ferry (1.35YTL/$1 each way) rather than a private boat, and charge you 40YTL ($30) for the privilege. The one advantage of the tour is that you get door-to-door transportation in clean, comfortable minibuses, and all transfers between sights.
For personal day tours of the city, I recommend nothing but the best: Credo Tours, Taksim Caddesi, Yonca Apt. 69/6, in Taksim (tel. 0212/254-8175), organizes personalized 1- and 2-day tours of the city for little more than cost. Factor in the cost of the museum admissions, the entrance fee for the hamam, and lunch, and you may even come out ahead (agencies negotiate lower rates for all of the above). Some of their prior requests include architectural tours of the city, Jewish Heritage tours, and art tours.