A Wonderful Stay
I absolutely loved The Inn at the Opera. Having stayed here on multiple occasions, I have stayed in every type of suite/ room from the smallest Ballet room to the Concerto room to the Opera room. Though all the rooms are wonderful for what your get (as in, don't expect to do your Jane Fonda Workouts in the ballet room - it is a super old building and people were much smaller then, after all), I recently stayed in the Opera room (largest suite) and it has been a wonderful experience. 
The Opera room is made up of a small entry with two chairs/table and a kitchenette, a sitting room which also acts as a secondary bedroom with the sleeper sofa with an attached a full large bathroom, and a master bedroom with an attached master bathroom. The Opera suite is the way to go if you have two couples, two singles that need their own sleeping armaments or a family of (4?) that has two kids that can sleep on the pull out sofa. 
The location of this Inn within the Hayes Valley at the Civic Center has become more desirable as the years have passed. Within walking distance are numerous (somewhat pricey) restaurants and shops. It is the perfect area for people who are willing to walk and explore and see what the neighborhood has to offer. And that is really what is area is - a neighborhood. If you are looking for chain restaurants then you will be out of luck. Staying at The Inn at the Opera and and allowing yourself to venture out only adds to the experience. Also, weather you have a car or not, Market Street is 2 blocks away and can catch the metro.
A new Norwegian restaurant opened at the Inn called Plaj (Play). I will let other people write about the details of the restaurant but the people who run the restaurant made me (and my guest) feel welcome when we showed up after a long day sightseeing looking for a nightcap to end our day (during business hours, of course). Ultimately their hospitality only added to the experience at The Inn at the Opera. 
Be forewarned that this building has no central AC or Heating. There are floor heaters provided but if you come on one of the rare scorching days (I say rare because during the Summer it is freezing - reference Mark Twain) then it may be toasty. Oh, and parking is roughly $25 a night additional to your hotel fee but apparently that is rather cheep in SF. I was lucky enough to find street parking 4 of the 7 nights of my stay.
Ultimately this is a great place to stay. Get the Opera room if you can but any other room will provide you with charm and comfort that you are looking for from an Inn. The staff is very friendly and if you time your return to the Hotel right you can even get a free cookie from the front desk.