We enjoyed touring several ships at the Maritime Museum, including The Star of India and some used in movies. Some of the exhibits were closed for renovations, but there were enough open for tours that we definitel got our money's worth.
This is the most fun place in SD in my opinion. You get to see how people used to live and work. You also get to play with simulator if you want.
One of the biggest museus in Balboa Park, it has excellent exhibits, but it is a LOT of walking.