Onedog has this one covered.
I think I might have been the one who originally mentioned Dinah's. As stated, it is "authentic 50's" not "sock hop 50's." I remember eating there and watched them bulldoze my minature golf course to make room for the San Diego freeway.
Also, I would second the vote for Pacific Dining Car *if* you are willing to pay high prices for great (but simple) food. This is a classic steakhouse, not one recently designed for the popularity contest. So they have good basic steak and fish and ... However, the steak might be $35 with no sides or salad. (Of course, this is cheap compared with Behrn's SteakHouse in Tampa, Florida). Dark, comfortable, and because they are open 24 hours, they are not rushing you out to "turn" the table.
I have been to the McCormick & Schmick's in downtown. Nice location. Not a fan because it reminds me of all the others in the chain.