Which tours of San Diego would you recommend during a three day stay?

There is so much to do and see in San Diego! Will you have a car, or just plan on guided tours? If no car, I would recommend The Old Town Trolley Tour that will take you around the city, a harbor cruise that will take you up and down the harbor/bay and under the Coronado Bridge, and if you plan on going to the zoo, take the bus tour and skyfari adnt hen walk to see the areas that interested you most. If you will have a car, drive to La Jolla, Coronado, Old Town and Downtown/Gaslamp.

Agree w/ SDGirl about the Trolley Tours. There was also a haunted San Diego bus tour we took ( I think it's the same tour company as the trolley but not sure) which was very entertaining and gave a nice overview of old San Diego. Have fun!

old town trolley & harbour

Sea World is also great fun.

Trolley Tour
Zoo
Sea World

Haven't been on the harbor cruise, but it sounds like fun, especially at sunset.