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Very common question. What are the best modes of transportation? What are cheap alternatives?
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It depends! How much money are you willing to spend? How fast do you need to get there? How tired are you willing to be when you arrive? San Francisco is known for its hills, but depending on what part of the city you're in, walking might be easy and cost-effective. I will walk if it's less than a mile, and give myself 1.5x as much time if it's going to be hilly. I'll only ride my bicycle in flat neighborhoods. When getting about on foot or bike, consult the San Francisco Bicycle Coalition's map to see elevation and bike lanes. BART serves very few parts of the city, but it sticks fairly close to its published schedules. You can plan your trip on Google Maps (they've imported all the times) or, if you have an iPhone, use the BART app to check real-time information. You can also follow @sfbart on Twitter for reports of delays. Muni serves much more of the city, but many of its lines don't adhere to a very strict schedule. In addition, there are more service changes as of December 5, 2009, so paper schedules and maps are probably out of date. Instead, check NextMuni.com before you leave your computer or from your mobile phone. Some bus shelters and most light rail platforms also show arrival times. These times are available on almost every line, and are calculated citywide using real-time GPS info.
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Muni and Bart are the easiest. The truth of the matter is that you can get anywhere in this city with those if you don't mind walking a couple blocks (or even riding your bike cause you can take those on buses with you). For all the places where it's really unaccessible to use either of those then you can cab it and it's not a big deal. The only time public transit becomes a pain is when it's after regular hours because the Owl lines are few and far between so if you're planning a late night out, make sure to have some cash for the cab ride home.
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i tired to merge this question and the one about cheap transportation.. did not work out exactly as planned, expand.. feel free to edit