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The San Francisco Chronicle's website is fun and pretty good - Sometimes you want the SF spin on the day's news, or you just want to know what's happening in the City by the Bay. SFGate is the San Francisco Chronicle's website, chock full of irreverent headlines, weird news, and plenty of Bush-bashing.
NYTimes is my favorite news source; I check it every day - I love the New York Times. They often break news, they coverage is generally comprehensive, well-informed and well-written. Mostly, I read their world news, US news, political coverage and business and technology sections. They also have good book reviews.