We have stayed at the Embassy Suites on PCH, the Omni and the Best Western on Ash Street. We could see the ship from our 9th floor balcony at the BW. There is a Holiday Inn directly across the street from the port. All had shuttles to the port.
Oasis of the Seas 5/21/11
www.portofsandiego.org/ has an overview of almost everything you need to know about the interaction between cruise ships and San Diego. A very extensive site.
www.sandiegocruiseport.com includes a listing of every cruise leaving from San Diego, parking lots with prices, outlines of local attractions, and much more.
www.sandiego.org/ has a listing of park-and-cruise hotels, which offer various packages if you stay at the hotel. Some offer free transportation between the airport and the cruise terminals. Other hotels allow you park your car in their lot for free if you stay at the hotel pre- or post-cruise.
San Diego Car Free: An entire web site devoted to seeing all of San Diego county without a car. Complete instructions on how to get anywhere using public transportation.