Best vacations for a parent with a three year old is one that allows parents and children to spend time together, and maintain some semblance of routine. (Disney is best saved for 5 years and up.) The zoo is a great idea! So are aquariums, science museums with activity areas for younger children, botanical gardens with paths, etc. Spending time outside with mom and dad, chasing balls, blowing bubbles, going to the park and being pushed on a swing, doing craft activities, putting up a tent in the yard or in the house, etc.
Family Fun Magazine has lots of great travel ideas, as well as crafts, party ideas, costumes, etc. for all ages.