I would just avoid the restrooms in most of the sit-down restaurants as they tend to be small, somewhat dirtier (from experience) and some do not have changing tables at all. The ones inside the parks all have changing tables that I can think of, in both the mens and womens bathrooms. They are usually quite large in size and kept very clean.
Also, the previous poster is right regarding family bathrooms. Disney only has companion bathrooms, and while a few of these have changing tables (I know a few in the Epcot World Showcase do, as does the one near Everest in AK) most of them do not -they are mainly for use by people who need the extra space of a companion bathroom (though some are VERY tiny) or are traveling with a party who could use assitance, such as a disabled person, or a parent traveling alone with several children, for example. I don't think I've seen a single companion restroom in MK with a changing table.
As others have mentioned, if you find yourself near the baby care center in a park (there is only one per park, not always convenient to travel back to for a diaper change) those are great to use and are staffed by helpful CM's.