There are a myriad of sightseeing tours of Stockholm available... by boat, by bus or on foot. The majority of the tours are provided by the company Strömma. If I was to recommend one tour to take then I would say that you shouldn't miss "Under the Bridges". It is an 1 hour and 50 minutes long boat tour that takes you around most of Stockholm, both the new and old neighborhoods. It really gives you a good overview of the city and Stockholm should really be seen from the water to be appreciated! The cost is 190 SEK (half off for children 6-11yrs) and is guided (8 languages to choose from) through earphones. Coffee and snacks are available on board. During the summer the tour leaves at the top of the hour (11am to 6pm) from in front of the Grand Hotel.
If you are looking for the most extensive sightseeing tour available, then "The Grand Tour" is your best bet. A bus & boat combination tour that lasts 3 hours 30 minutes and costs 420 SEK (half off for children 6-11yrs). Departs 10.30 and 12.30 daily from Gustaf Adolf's Square (after July 1st they add a tour at 2.30pm as well).
With the Stockholm Card you get discounts on some tours (not the above mentioned tours) like the Royal Canal Tour, Panorama bus tour and the Open Top bus tour.