It's a toss up between two local non chain restaurants. Angelos Hollow Inn with excellent Italian food, and The Wilderness Lodge with a great setting and the best wings.
Locally there are a couple establishments that I have yet to have a bad experience.
The Wooden Spoon
The Friendly Toast
Harvey's Bakery and Coffee shop
La Festa Pizza
Spur Steak Ranch :P
Toss up between two local establishments. JC Lobster Pot and Down the Hatch Unfortunately Down the Hatch was badly damaged during hurricane Matthew, and due to city permits and insurance hassles has yet to open back up. They are getting closer though!
Benu on Hawthorne St in San Francisco. One bucket list item every food enthusiast must have.
I know you are gonna think I am crazy but I base my "favorite" resturant on customer service. Chili's has the best customer service just about every time we went and just about every one we have tried. (Except for the last time we went. It sucked! The menu, the waitress, the customer service and the food!)
Buffalo Wild Wings