San Diego County has numerous museums for a wide variety of interests. And many of them are free, have free resident admission days once a month, or have low-cost admission rates. This is not a comprehensive list of all museums in San Diego County, only those that are low-cost or free (at least once per month).
Balboa Park
Balboa Park has many museums and attractions, most of which are free on one Tuesday per month for San Diego residents. They generally are crowded on the free Tuesday, but if you arrive early, it's not too bad.
Timken Museum of Art
Admission to the Timken Museum of Art in Balboa Park is always free. Open Tuesday - Saturday 10:00am - 4:30pm and Sunday 1:30pm-4:30pm.
San Diego Children's Discovery Museum
This hands-on children's museum in downtown Escondido has both indoor and outdoor activities, including a fenced off area for toddlers and babies. They have a themed exhibit that changes throughout the year and ongoing events that are free with admission. Although admission is $5/person for anyone 1 year and older, annual family memberships start at $85 (just over $7/month). A family membership includes 2 adults and all children in the immediate family, plus 2 free passes to share with friends. Parking is free.
San Diego Archaeological Center
Located 1.5 miles East of the Wild Animal Park, the San Diego Archaeological Center Museum explores how people have lived in San Diego County for the past 10,000 years. It has changing exhibits and includes hands-on activities. It is open Tuesday through Friday 9:00am - 4:00pm and Saturdays 10:00am - 2:00pm. Admission is a suggested donation of $2 per person or $5 per family.
Flying Leatherneck Aviation Museum
The primary purpose of this museum at MCAS Miramar is preserving the history of the Marine Corps Aviation. Open Tuesday - Sunday 9:30am - 3:30pm, admission is free, but donations are welcome. The museum has both indoor exhibits as well as an outdoor area averaging 25 vintage aircraft.
The Lux Art Institute
Located on El Camino Real in Encinitas, the Lux Art Institute is free to everyone under 21 and to anyone who rides their bike to the Lux. Admission for everyone else is $10.
Escondido History Center
Located in Escondido's Grape Day Park, the History Center includes some historic buildings and a recreated blacksmith shop where volunteers are usually working during museum hours. Open Tuesday through Saturday 1:00pm - 4:00pm, the highlight for many kids is probably the H-O scale model railroad that runs inside the Pullman Railroad car located next to the 1888 Santa Fe Depot. Admission is free.