Wow this question has so many answers which may all be correct. Single family residence, 2-4 units, Commercial type property, land for speculation, fractional interest, and on and on. I guess it depends on what type of property you're looking for, how many people will be investing in it, what price range you're looking in, recourse or non-recourse, and how long you plan on holding the investment for.
You'll need to consider things like, cash on cash return, CAP rate, gross multiplier, vacancy factors, buying a property needing some work, or a property needing much work, master metered, access, parking, your anticipated level of involvement, and again on and on.
However, in my experience the closer you get to the coastal areas the more you'll pay for property in general, and consequently the lower the CAP Rates. If you head out to the east county areas you will usually find higher Cap Rates and will most likely get more for your money.
I guess the best way to figure out where you should buy real estate in San Diego is to first determine what you're looking for in a property; consider the above information and then move towards the coast or towards the east county based on the value you think is best for you.
I hope this has been helpful!