The main destination for shared rooms and roommates - as for most other things, too - is Craiglist:

• Craigslist - room & shares San Francisco 
• Craigslist - room/share wanted San Francisco 
• Craigslist - rooms & shares in San Francisco & Bay Area 
• Note: Restrict your search by area, neighborhoods and min/max rent to help you find the right match

Other useful apps & sites:

• Crashpad: find roommates and rooms
• Lovely: simple and intuitive website and app to search for apartments, set alerts to be notified
• ApartmentList: huge search engine for apartments, better layout than Craigslist
• PadMapper: apartment hunt via map
• Roomidex: find roommates amongst your friend's network via Facebook
• Livewith.us: helps you optimize your Craigslist postings

More information:

• Curbed SF - On the Hunt for Roommates or an Apartment? Check Out these Craigslist Alternatives 
• Oh Happy Day - 5 Tips for Apartment Hunting in San Francisco + Our Story 
• Berkeley Parents Network - How to Find Housing in the Bay Area 

Image by 55Laney69 via Flickr

Average rent in the Bay Area:

• Shared apartment: ~1,000 USD
• Studio/1-bedroom apartments: ~1,600 USD
• >2-bedroom apartments/(town) houses: >2,500 USD

Costs of utilities:

• Often utilities come extra to the rent (e.g. water, gas, electricity, waste management, gardening)
• For a small house (2 bedroom place) the utilities cost might be around $180 -$250
• for an apartment you might look at as little as $70

Bay Area communities by descending price range & common desirability:

• Ridiculous: Atherton, Woodside, Los Altos Hills, Portola Valley
• Expensive: Palo Alto, Los Altos, Menlo Park
• Pretty expensive: Mountain View, Sunnyvale, Cupertino, Los Gatos
• Somewhat expensive: San Jose, Campbell, Redwood City, Foster City
• Not cheap: East Bay
• Developing: East Menlo Park, East Palo Alto (roughly the area east of US101)
  Note: The times of East Palo Alto being the city with the highest homicide rate in the US are over (1992), but it's still developing, check the details on city-data.com, as mentioned below.

How to find the right place on Craigslist?

• Almost all accommodations are posted on Craigslist, brokers & realtors seem rarely to have unique offers
• Main rule: reply instantly if you find a potential match, good offers are usually gone within hours
• Example: you are looking for a 2-bedroom apartment within a 20 minute commute from Palo Alto
• Select the two relevant areas in separate windows:
• Peninsula: http://sfbay.craigslist.org/pen/apa/
• South Bay: http://sfbay.craigslist.org/sby/apa/
• Select the applicable neighborhoods by clicking on '[+] all neighborhoods', to stick with the above example of around 20 drive from downtown Palo Alto:
• Peninsula: Atherthon, Belmont, Los Altos, Menlo Park, Mountain View, Palo Alto, Portola Valley, Redwood City, Redwood Shores, San Carlos, San Mateo, Woodside
• South Bay: Cupertino, Mountain View, Sunnyvale, Santa Clara
• Check the Bay Area map on SFGate to see where the Neighborhoods are located
• If you're unsure, check the distance to your workplace from your potential future home using Google Map
• Select '2+ BR' to look for objects with at least two bedrooms (living rooms are not counted)
• Enter your max. rent to restrict the selection and even min. rent to throw out fake offers

How to find a place in San Francisco?

• SF Startup Survival Guide: How to Find an Apartment in San Francisco
• The Bold Italic: How to Conquer Apartment Hunting
• Oh Happy Day: 5 Tips for Apartment Hunting in San Francisco
  

Hints:

• Get insights on average income, house prices, crime rates, etc. on city-data.com (example: Palo Alto)
• Always visit the the place before renting (at least for longer than just a few weeks), attractiveness of locations can vary drastically from street to street, Google Street View can you give you at least a first indication
• Helpful apps/websites to find housing:
• Lovely
• Padmapper
• Zillow 
• Trulia 
• Redfin
• Take the traffic into account, when planning your commute - San Francisco has the 3rd worst traffic in the US (applying similarly to the whole Bay Area, e.g. US101): USA Today

• Get a good antenna and a receiver (e.g. European systems seem to be incompatible):
• Mohu Leaf Paper-Thin Indoor HDTV Antenna - review
• C2 ClearStream Antenna - review
• Check your TV Signal: TV Fool Choisser Channel List 
• Or get Aereo in case legalized and as soon as it is available in the Bay Area
• Watch via app or web:
• Hulu (free)
• The CW (free)
• Netflix (7.99 USD/month

The US' TV and telecommunication market is known for its high monthly costs compared to other countries and it comes with a huge variety of combined offers which can leave the freshly moved geek simply confused. 

E.g. often 24 month contracts are offered for a relatively low monthly payment, which increased after 3 months and again after 12 months - both only mentioned in tiny letters below the main offer - or only in combination with expensive channel packages.

To keep the costs low in the beginning I did the following:

• Getting the cheapest Internet-only connection (calculated over the whole 24 month period, to be able to compare the overall costs - in our case the cheapest was Comcast)
• Get TV over the air (see here) and via apps
• No phone landline
• US Calls: use mobile phone
• International Calls: use Voice over IP (in my case with a free German number from sipgate using the app Groundwire)

Image by Thomas Leuthard via Flickr