I guess it depends on what location you are asking about Onepixel. The Rasputin in San Jose by my house seems to not get much in the way of used vinyl and it's selection is nothing when compared to the one in Berkeley, however it's far better than the one that is in San Leandro, the one in Stockton and the one in Walnut Creek, who get almost no used vinyl and give you the feeling of deja vu as they all carry the same exact new vinyl.
As for Amoeba, I really like the one in Berkeley and find quite a bit of stuff there and the one on the Haight is incredibly huge, but the problems they face is the stiff competition from collectors who live in the area who can scour the racks on a very consistent basis. People like you and I are left with what hasn't been scavenged...also for the good stuff, they are very expensive most of the time.
For the best record store in my area, I would have to say that it would be Street Light Records on Bascom. The best overall store would have to be Amoeba, but I am torn on the merits of Berkeley versus SF. If pressed to choose, I would pick Berkeley as its closer...
What is your favorite?