Roughly in order from north to south...
Airport (SFO) Restaurants: see SF Eater's Guide to San Francisco International Airport Dining
Dim Sum in Millbrae: Zen Peninsula or Hong Kong Flower Lounge (rec'd Michelin)
Gintei (San Bruno) - sushi rec'd Michelin
Pescadero: Duarte's - pronounced "dew-ahrts", an old-as-heck bar/restaurant with a lot of charm, try the half-and-half soup (it's not on the menu), crab melt, and save room for pie!
*** Half Moon Bay: Dad's Luncheonette - a traincar converted into a take-away kitchen that serves amazing lunches Thursday through Sunday from 11 to 4; chef Scott Clark used to work at fancy Michelin-starred places like Saison so he uses top-notch ingredients in interesting ways (but still casual & not too expensive)
*** Half Moon Bay: The Barn - fancy burgers (pastured-raised beef, etc) in a hip converted barn setting
Half Moon Bay/Montara Beach: La Costanera - Peruvian...previously had a Michelin star?
***Mack's BBQ - 1754 Laurel Street, San Carlos 650-592-4BBQ, some of the best brisquet, pulled pork, and tri-tip in the Bay Area
?? Camper (Meno Park) - california cuisine, rec'd Michelin, dinner only
Flea Stret Cafe (Menlo Park) - pretty upscale, organic, sustainable ingredients, California cuisine, Yelpers like short ribs, lavender lemon drops, crispy sardines, beet salad, and smoked trout, rec'd Michelin, dinner only, closed Sun/Mon
?? Georgian: Bevri - rec'd Eater
?? Barcelona/Tapas: Telefèric - rec'd Eater
Pizza/Italian: Terún - pretty good pizza, excellent appetizers (including burrata), rec'd Eater
Upscale Indian: ROOH - also a branch in SF, dinner only except Sat/Sun
Upscale Cal-Indian: Ettan - dinner only except Sun, rec'd Eater (more here), Michelin
French Bistro: Zola - dinner only (but opens early at 3 PM), rec'd Michelin
Pizza/Italian: Italico - dinner only, rec'd Michelin
Cuban: La Bodeguita del Medio - folks online rec'd ropa vieja, arroz con pollo, tierra y mar, rec'd Eater
Cal/French: St. Michael's Alley - when I was at Stanford this was the place you'd take a romantic date; it still looks nice/romantic although perhaps a little bit dated?, rec'd Eater
Italian: Vina Enoteca - rec'd Michelin
New Orleans: Nola - rec'd Eater
Upscale Vietnamese: Tamarine - great Vietnamese-inspired food, although a bit pricey, try their "fish in a bag", rec'd Eater, Michelin
Upscale Greek: Evvia Estiatorrio - awesome appetizers; try the cheese, etc., also a branch in SF, rec'd Eater, Michelin
Burmese: Rangoon Ruby - nice tea leaf salad
casual stops:
Ramen: Ramen Nagi Palo Alto - was their first US location, rec'd Eater
Israeli/Mediterranean: Oren's Hummus Shop - 261 University @ Ramona...now has outposts all over the Bay Area, rec'd Eater
Jamaican: Coconuts - rec'd Eater
Breakfast/brunch: Hobees - fun old-school place for brunch
Casual Indian/Pakistani: Zareen's - rec'd Eater
Old School American: Palo Alto Creamery / Peninsula Grill - diner fare & milkshakes, decor makes you feel like you're in the 1950s/60s, rec'd Eater
Bakery: Manresa Bread - outpost of Michelin-starred restaurant
expensive haute cuisine:
Protégé - rec'd Eater, 1 Michelin star
?? ASA North (Los Altos) - looks like a slightly more casual version of the Los Gatos ASA South restaurant, looks nice, dinner only
Doppio Zero Pizza Napoletana - pretty decent Neapolitan-style pizza and a few other dishes, rec'd Michelin
Aurum (Los Altos) - somewhat upscale Indian place rec'd Michelin
Sushi Tomi - rec'd by many, good specials, fresh fish
Haute Cusine French: Chez TJ - expensive, haute cuisine tasting menu, 1 Michelin star
Cascal - tapas
Amber India (Los Altos) - nice neighborhood Indian place with classics like tikka masala
Bakery: Manresa Bread (Los Altos) - outpost of Michelin-starred restaurant
Kappo Nami Nami - rec'd by chowhounds, Kyoto-style, like izakaya
Very Fancy Japanese: Hiroshi (Los Altos) - expensive but looks very nice
Middle Eastern: Dish Dash - nice mix of dishes, fun for a group, vegetarian friendly
Japanese: Tanto - somewhat casual, good online reviews
Japanese: Rokko - also pretty good reviews
Eater also has a list of Chaat places in Sunnyvale
Korean places galore: Jang Su Jang, Silla Korean, Chungdam, etc. (probably the highest concentration/best in the Bay Area)...see Eater's list for more
Din Tai Fung - outpost of the famous Taiwanese dumpling place in the Westfield Valley Fair Mall
Lady M Cake Boutique - outpost of the Japanese pastry shop, known for their "mille crêpes" desert (many layers of thin pancakes with cream in between...I tried it in Shanghai and it was great), also in the Westfield Valley Fair Mall
Eastern European: Euro Grill - looks interesting
Japanese: Amakai
Cult Ramen: Ramen Nagi
coming soon: Eataly San Jose...
Manresa (Los Gatos) - expensive farm-to-table tasting menu by chef David Kinch, 3 Michelin stars
? The Bywater (Los Gatos) - New Orleans-style food, Michelin Bib Gourmand
? ASA Restaurant South (Los Gatos) - looks like a fun fusion-y place with a fair amount of pasta, Michelin Bib Gourmand
Cult Ramen: Ippudo (Cupertino)
Upscale Mexican: Luna Mexican Kitchen (Campbell) - rec'd Michelin
California Cuisine: Orchard City Kitchen (Campbell) - rec'd MIchelin
Daly City
Dim Sum: Koi Palace, Moonstar, Tai Wu Mr. Fong's
Burmese: Little Yangon, Burma Cafe
South San Francisco
Mexican: Rancho Las Trancas - South SF
El Charro - South SF (Bolivian)
Burlingame
Vietnamese: Cherimoya - bahn mi, garlic noodles, rec'd by chowhound
Burmese/Chinese: Mingalaba - 1213 Burlingame Ave, chowhounds rec'd the "house special noodles"; also try tea leaf salad
San Mateo
Sushi Yoshizumi - 2 seatings per night (except Mon/Tues) for $145+ tasting menu, rec'd by Googler, need to book ~2 months ahead...*cannot* do gluten-free
Ramen Dojo
Sushi Sam
Hotaru (homestyle japanese)*
Sweet Breams (dessert teriyaki)
Wasiiki (peruvian...changed owners?)
All spice * - 1 Michelin Star 2015
Viognier (on top of Draegers) [high end]
Wakuriya (Crystal Springs shopping center, upscale Japanese) - 1 Michelin Star 2015
AcquaPazza?
Osteria Coppa?
Tannourine - 120 W 25th Ave
Beijing Regional Chinese: Everyday Bejing
San Jose
Ethiopian: Zeni's
Islamic Chinese: Chinjin Eastern House
Peacock Indian - good biryani (also branches elsewhere)
Mountain View
Kabul (Afghan)
Yam Leaf (Salvadoran)
Himalayan Kitchen (Nepalese/Indian)
Sakoon (Upscale Pan-Indian) - a bit fancy but nice
Shezan (Pakistani/North Indian) -
Shana Thai (Thai) -
Tommy Thai (Thai/Cambodian) - most of waitstaff is Chinese but chef is Cambodian
Krung Thai Mountain View (Thai) - curries, "authentic", although some people like the San Jose location much more
Amarin Thai (Thai) - reasonably-priced, nice
Le Petit Bistro (French) - classic dishes, Yelpers like lobster bisque, liver paté, and coq au vin...nice, romantic atmosphere
Chef Zhao Bistro (Sichuanese) - rec'd by several CHs (see long discussion), lukewarm Yelp reviews...also San Mateo location
Sajj Mediterranean (Middle Eastern) - spin-off of a food truck, offers inexpensive shawarma, falafel, kebabs, etc.
ViVe Sol (Mexican/Pueblo)
Agave (Mexican) - especially regional Mexican (from Oaxaca/Yucatan) and pre-Columbian Mexican, opened ~2012,
Vietnamese/Fusion: Xanh - a fancier take on Vietnamese food, a little bland but generally tasty, accommodating for large groups
More Peninsula notes: chowhound commuting list, chowhound south bay list. This guy's impressive list of (mostly Asian) South Bay places.