It depends on why you are coming to San Francisco. Since you wrote you may be living here this Fall (and if it is only for 2–3 months) try looking for a sublet or a share situation. It will be more expensive than living in the suburbs but if it is short term, you’ll want to spend more time living in the City and less time commuting.
The prime neighborhoods for getting in on the action for 20–30 somethings are Russian Hill, Telegraph Hill, North Beach and the Marina District. There are some short term rental places around Union Square and SOMA but in those areas you can walk 3 blocks and be in a less desirable neighborhood. San Francisco is so compact, people think they can walk everywhere. It is usually OK if you know how to “City walk” but don’t meander along draped in cameras in poorer neighborhoods. You might find something reasonable on the west side of the City in the Richmond and Sunset districts, which are more family neighborhoods. The west side is the most like the 1940’s/50’s with few chains and very quiet after 9 pm. Just perusing Craig’s list temp sublets run from $600—!000/mo for a furnished room.
If on the other hand you are moving to San Francisco, your best bet is the suburbs. If you don’t have a job and you are not a lawyer or doctor or other professional, you may have a better chance of finding a job in the suburbs. Some of the corporations have moved to Walnut Creek, San Mateo and Hayward. If you are coming here to find a job in the public sector, you might want to try in 2011. If you lived and worked in the suburbs, you could still use the City as your social base. We have pretty good public transportation into the City