Where to Stay? 
Choosing Hotels et. al. in and around San Francisco

         FYI: hotels in San Francisco, Oakland, San Jose, many near SFO  and others add to your final bill a Hotel Tax, officially a "transient occupancy tax."  If budgeting closely, you may want to ask about this while booking your reservation.
         Some visitors planning longer stays have found AirBnB and similar on-line services offering houses, condos, and apartments for short-term rental a satisfying option...but with a rental, when you're looking for help--what's the best time to take a cable car ride? or is Alcatraz really sold out?--you're really on your own.

"Downtown": Union Square, The Financial District & Nob Hill
Pros: easy access to all major transit corridors and taxis; amenities associated with historic
    "grande dame" and boutique  hotels; many high-end restaurants and fast-food outlets,
    and luxury purveyors like Armani and Neiman Marcus; walking distance from the
    Moscone Convention Center; proximity to the Theater District...and your room if needing
    to catch a nap during the day or a concert/show after dark
Cons: definitely "downtown" with frequent crowds, usually harmless panhandlers; Nob Hill
    itself a steep climb from Union Square shopping but offering Grace Cathedral,
    panoramic vistas
cf. Larkspur, Chancellor, Westin St. Francis, Fairmont, Mark Hopkins, Stanford Court

Northern Waterfront (Fisherman's Wharf, Ghirardelli Square)
Pros: proximity to sea lion colony at Pier 39 and the Exploratorium (world-class science
    museum), Ferry Building's "farm-to-table" markets; views of Alcatraz & Golden Gate
    Bridge; information for and starting point of many activities popular with visitors--
    rentals of GoCars, bicycles, Segway tours, big-bus tours, etc.; Boudin's Bakery (home of
    sourdough bread); the unique Musee Mechanique; lots! of souvenir shops; many seafood
    restaurants
Cons: farther from BART (interurban transit), Golden Gate Park, most residential
    neighborhoods; very "touristy" and crowded on holidays and during high
    season...children will often enjoy the un-usual sights (like human "statues"),
    adults less so

SFO (Airport)
Pros: often less expensive, with most immediate access after a long flight
Cons: if intending to sightsee during the day or enjoy SF nightlife, requires finding taxis, Lyft, Uber or BART for half-hour
    to 40 min ride into, out of downtown SF

on Lombard Street (b/w Van Ness and The Presidio)
Pros: less expensive motels; nice neighborhoods for walks nearby, especially historic Presidio (a forested park); walking
    distance to many excellent restaurants on Chestnut & Union Streets
Cons: heavy traffic during rush-hours; parking (unless provided by your lodging) hard to find and expensive; minimal 
     ambience

Neighborhoods away from Downtown
(Pacific Heights, Cow Hollow, The Haight, The Castro, Japantown)
Pros: much more contact with locals and neighborhood gems: some hotels (e.g. Drisco) and B&Bs (e.g. Union Street Inn)
    have unique charm
Cons: will require time to travel on local transit/Lyft et. al. to the more popular attractions

SOMA (South Of Market Area)
Pros: close to Moscone Convention Center, MOMA (Museum of Modern Art), Westfield Mall (Nordstrom, Bloomingdale's);
    15-minute walk to Giants' stadium
Cons: 1-3 long blocks' walk to Union Square shopping

Oakland, Berkeley & Emeryville (east, other side of the Bay)
Pros: less expensive, quieter (other than Big Game and graduation weekends); flights into OAK may be cheaper than SFO;
    near some of region's best restaurants; closer access to Napa Valley wineries
Cons: requires using BART (interurban transit) or AC busses to reach San Francisco attractions which can add 40 minutes
    or more to your travel time both ways

Sausalito (north, directly across the Bay)
Pros: quiet; shuttle to Muir Woods (check which days); panoramic views from some venues; near Cavallo Point (former
    military base now upscale resort, next to Golden Gate Bridge)
Cons: bus and ferry access to The City may be challenging during busiest weekends for tourism

Silicon Valley (Palo Alto, Sunnyvale, Mountain View, San Jose...30-45 miles south, on The Peninsula)
Pros: if a taxi ride from Caltrain, then easy though distant access to San Francisco...Levi's Stadium relatively close
Cons: if far from Caltrain, requires rental car or long VTA rides to reach most places of interest