About.com on quality lodging
Read "small, affordable hotels a little off the beaten track." which describes the Nob Hill Hotel. You can also read that review at the Nob Hill site. Other gems in the area include the Fitzgerald Hotel in Union Square, and Oreilly's, an awsome original Irish pub. Also check out the Hidden Vine Wine Bar, a truely spectacular place. Lodging info can also be found here.
Check out the Nob Hill San Francisco blog for more info on Nob Hill, and the North Beach blog for information on North East SF. WikiTravel's SF section also has a good collection of resources on things to do in the area.