I've been looking for a good metric to compare prices across cities, to estimate where the housing boom "happened" the most. It seems like the data becomes cleanest at about 10 years ago. For instance, in comparing cities in California: in 1998 Los Angeles was coming out of the early-1990s housing price crash, whereas San Francisco hadn't realized many of the rewards from the tech boom.
If you wait until 2000 (which Case-Shiller is based on), LA and SF have diverged wildly (which makes SF look less bubbly than LA). LA's growth doesn't start until after 2000, whereas Silicon Valley has a pop in 1999 and 2000.
The graph that convinced me of this is First Republic Bank's "Prestige Housing Index": Here's LA and SF. Quite a difference. (FWIW: I think this index is pretty much bunk back if you go back to the 80s, because they thresholded properties costing >$1 million, and there just weren't that many of them back then.) Since the 90's, though, things look interesting, and the "prestige" data bears out my claim that Prime areas haven't seen their doomsday yet.
Whether this means that Silicon Valley/SF will retain some of their gains, whereas LA will lose more of them, I don't know.
But, this is one of the reasons I like the ten-year Zillow graph to compare zipcodes. A lot of the stock market madness from 1999-2000 seems to be canceled out if you go back to 1998.