Affordable, great location, but noisy and stuffy
The main attraction of the Wharf Inn is the price/location combination-- It's an easy walk to Pier 39 and the other Fisherman's Wharf Area attractions. Low room prices and free parking make it very cheap for the area.
Unlike some other reviewers, we found the staff to be polite and helpful and the rooms very clean. Note that this is an upgraded motel, not a resort, so don't expect room service. 
Basically, this is a good place to stay if you plan to be out seeing San Francisco and not spending a lot of waking time in the hotel.
Our only big negative was the noise/ventilation combo. There's not much ventilation if the heat isn't on; the windows have panels that will open and give you more air circulation, but that also lets in outside noise, and two sides of the hotel face busy streets. Probably not an issue in winter, but in summer, if you're a light sleeper, pack some earplugs.