Going away for a week-end or a week is much easier when the travel time is only a 1 hour flight, and even though San Francisco may be in the same state, it is a world away in style and sensibility. Quikbook has some great deals if you book by this Friday before 5pm EST.
If you like being in the middle of town, then book the Hotel Nikko; it is just 1 block from Union Square with rates starting at $120 per night (50% off the regular rate). This hotel has a 24 hour fitness center, enclosed atrium pool, Japanese rock garden, and marble bathrooms. Keep in mind they have a fee for spa and pool use, but if the weather is cold (as it usually is in SF this time of year), it may be worth a few dollars for some recreation in a warm enclosed environment. Union Square is central to both shopping and theater, so this is the place to stay if you want to walk to the stores or shows and catch a cable car to Fisherman's Wharf.
If you prefer a more residential upscale neighborhood with spectacular views, you might prefer the Huntington Hotel and Nob Hill Spa with rates starting at $150 a night (40% off the regular rate). The hotel is on a cable car line, so being upscale doesn't mean you are stranded up on a hilltop, but it is worth noting that this hotel is on a very steep hill, so come prepared with your walking shoes or get a ride to your destinations away from the hotel. This smaller family owned hotel has paid attention to the details that make you feel pampered, from the plush robes to Irish linens, but they have kept in mind that you may want to work, so their antique desk has plenty of room for your laptop, has a dual line phone and wireless internet (for a fee). Some of the things I like best about this hotel is that they still offer a complimentary newspaper, twice daily maid service, and complimentary fitness access (Hotel Nikko might want to take notes here).
These are both non smoking hotels, so save your cigars for a trip to Miami.