BKB Update, 12/08: The Ramada Plaza is once again the Hotel Whitcomb.  And see my more recent post on the Hotel Americania.  Yesterday I wrote about the St. Regis San Francisco, naming it the best hotel in San Francisco.  But if it doesn't fit in your budget, here are two other great options that might.

The Orchard Garden Hotel is
California’s first hotel
built to the nationally accepted standards for green buildings
developed by the U.S. Green Building Council (USGBC) –  in order to
earn a coveted “Leadership in Energy & Environmental Design”
(LEED®)  certification.  But what's most impressive is that you might not know this was a green hotel if they didn't tell you.  It's a great example of how green practices can be incorporated in a service and amenity-driven industry without compromising comfort, style and convenience.  Although the hotel
was still installing some finishing touches while I was there last month, it is clearly ready for the modern traveler, with free Wi-Fi, Hi-Def LCD TVs, DVD players and iHome iPod docking station alarm clocks.  Not everything in the hotel is organic, but every design and operational decision is informed by a green consciousness.  And with rates starting at $153 including a European breakfast, you'll be saving more than just the environment when you stay there.

My third choice for SF's best hotels is the Ramada Plaza Hotel, where rooms are often available at $89.  Built as the Hotel Whitcomb in 1916, the early 20th-Century design of the hotel lobby is surprisingly opulent, if dated, but the modest rooms are clean and comfortable, and offer free Wi-Fi access.
The hotel's location at Market and 8th Streets can be a little sketchy, with a high concentration of homelessness and run-down buildings in the immediate few blocks around it.  But it's also extremely convenient to public transportation, including the Civic Center stop of the efficient BART train from SFO or Oakland airports, and literally just three or four blocks from many of the city's more gentrified attractions.