Fairmont Heritage Place

Many of the hotels near Fisherman's Wharf/Ghirardelli Square don't really give you a lot for your money. This Fairmont property has brought a much needed truly nice hotel (without a theme!) to the area. The feel of this place is more or less like your own apartment and some of the rooms have an absolutely killer view. I used to live in a building very near by that had the same view so I know what I'm talking about. Still rather low key given the location as word hasn't spread quite yet. If you're looking to stay in this area and aren't on a strict budget, this is the property you need to book.

(View will be similar, but this was not taken at the Fairmont.)

http://www.fairmont.com/ghirardelli

Hotel Drisco

2901 Pacific Ave (between Baker St & Broderick St)

If you want to feel like a local during your stay, I'd say that this hotel is your place. Located in the fabulous neighborhood of Pacific Heights, you'll probably feel more as though you're in your own apartment. I recently had friends stay here and they loved it. If you don't mind being out of the way, this is a place I highly recommend considering. As someone who grew up in this neighborhood, I have to say that I think you'll quite enjoy "living" here for a few days.
http://www.jdvhotels.com/drisco/

Where to Stay: Part 3

Nob Hill

Pros: Residential feel, quiet, close enough to downtown to be a good jumping off point, great views.

Cons: More residential, steep climbs up/down hill if you're walking, hotels can be expensive.

Hotels to consider:
The Ritz-Carlton - name pretty much tells you what you're in for. Great spa. Highly recommend the Dining Room even if you choose not to stay there. The tasting menu is a must for any foodie.

The Fairmont - An original San Francisco landmark! Beautiful common areas, nice rooms, great views from certain rooms. Cable car stop nearby.The Stanford Court - Likely the most "budget" friendly of the Nob Hill hotels. Older. Could likely use a renovation in the rooms, but perfectly acceptable if you get a good deal. Cable car out front.

The Mark Hopkins - Top of the Mark is located here and a great place for drinks even if you choose not to stay here.

The Huntington Hotel -Home of the Nob Hill Spa, which I highly recommend. One of the "big four" hotels.

Where to Stay: Part Deux

The Embarcadero

The Embarcadero is one of my favorite areas in San Francisco. Close to the water, great area to walk or jog, with absolutely stunning views.
The Pros to staying in this area: Beautiful water views without the madness of Fisherman's Wharf, quiet at night, very calm, beautiful area.
Cons: Quiet at night, not as central to downtown as Union Square, not too many hotel choices.

The hotels:
The Vitale - Luxury boutique hotel. Great restaurant and bar and one of my favorite after work spots (I'm sure my stalkers are taking notes. ;) ) Lovely views and amazing suites. I was lucky enough to stay in a panoramic suite (see photo) one weekend and it was one of the best experiences I've ever had. It is small and intimate but with the luxuries of some of the more well known chains. Small, but nice spa. Simply put, you can't go wrong here. Cable car 2 blocks, historic street cars and buses stop next door.

The Hyatt Regency - Typical Hyatt hotel. California Street cable car stops right next to the hotel. If you've stayed at one Hyatt (or Hilton, or other similar chain) you know what this is all about.

The Harbor Court Hotel - Not as great a location as the first two mentioned but you can still get around by walking a few extra blocks.

Where to Stay?

Union Square (and nearby)
Pros: Very central to pretty much everything you'll want to see, nice hotels, get more for your money hotel wise than Fisherman's Wharf.

Cons: Extremely busy area, quite a few beggars.

Hotels in the area that are budget friendly:
The Chancellor - this is really one of the best as far as your budget friendly options go. It is an older historic hotel with a great location.
The Powell - Steps from the Powell Street BART station and right next to the cable car turn around. You may want to specify you would like a room facing away from Powell Street or the cable cars may keep you up late and wake you very early. Very basic property. Location is the best thing is has going for it.
Hotel Adagio - Hipster scene, good restaurant, good location.
Westin St. Francis - If anyone is fimiliar with the Fatty Arbuckle scandal, this is the hotel! You can even stay in the notorious suite if you have the funds. That said, to those on a budget, you can often get this property on priceline for a very reasonable rate and you can't be the location.

If you have more to spend consider the following:
Campton Place - Luxury boutique hotel right on Union Square. Lovely on site restaurant.The
Four Seasons - The name pretty much tells you what the hotel is all about.
The Intercontiental - Just opened in 2008 and supposed to be extremely nice. Within walking distance of Union Square.
The St. Regis - Within walking distance but not technically Union Square. Great luxury hotel with spa to match.Don't hesitate to ask for info if you have a specific hotel in mind. It is impossible to list them all here!