For the last couple of years, I haven't needed this information so don't know if it's still the case. One of the nice things pre-the-9/11 cutbacks which derailed SFO-ONT then was that the northern California to southern California fare rules often included ONT as a transfer point, which made it that much easier to work up intra-CA segment runs. E.g., you could do things like: SMF-SFO-SBA-LAX-ONT-SFO-SMF, etc., etc. I don't know whether the fare rules still allow these routes/transfer points. (I used to often sneak in SBA into ex-SMF or ex-SJC routings to SNA/ONT for little/no fare difference, but playing around tonight I couldn't find anything like that -- and Expedia's fare rules used to make it very easy to check but no longer....)
Lots of interesting thoughts on the thread about why the disparity, but it still seems very strange to me!
(I also remember back in my intra-California mileage/segment running days that SFO-LAX-SFO was virtually never a cheap ticket, and routings ex-SMF or ex-SJC or ex-OAK were substantially cheaper to LAX. Things change.)