My favorites:

In-N-Out (obviously)

Kirk's Steakburgers-small chain with 2 (3?) locations in the Bay Area. Really juicy steakburgers, with excellent toppings, and good garlic fries/onion strings.

Steak-N-Shake: Been to Indiana twice, and I absolutely love this place.

Burgerville is great as well. I had it a couple times when I was in Portland last year, and it was excellent.

Armadillo Willy's BBQ. It's nowhere near as good as 'real' bbq (Texas, KC, Memphis, etc), but it's the best I've found in the Bay Area.