These are the officially authorized ones: Farmers Markets in San Diego - Find locally grown produce: San Diego County Farm Bureau
I like the Hillcrest and Little Italy ones best because they are near my house. Little Italy also has good musical entertainment going and they have a booth that sells freshly shucked oysters. I also go to the Golden Hill one because that is where I the pick up location is for my grass fed meat CSA. It's a smaller market but it gets some interesting vendors like this guy who makes the best home brewed kombucha and this old Morrocan guy who sells great spices, organic lamb sausages, feta cheeses, etc.