I booked this room for about 3 months while interning in SF. It was a great room and definitely felt safe staying there. As a woman traveling alone, I never felt unsafe in this Inn. There is a code to get into the Emperor Norton and I could always leave my windows open to circulate air (Rooms are on the second floor and up). Safety was my biggest worry about staying downtown, but I definitely felt safe there.
The room was very clean! I never once had a complaint while staying there. I had to leave earlier than expected due to a hurricane hitting my hometown, and Hiromi was great to work with. She had great brochures on attractions around and even recommended a very nice laundromat 3 blocks away that I could do my laundry at.
The Emperor Norton Inn was very quiet and everyone was respectful of each other. The street below is a busy street and there will be noise outside the building- that's the city for you. I'm the type of person who has to have noise in order to sleep, so the noise did not bother me. If you have to have silence in order to sleep, bring ear plugs.
The location of the Emperor Norton is pretty much perfect. It was a quick 10-15 minute walk to Market street, where I was interning. It is about half a mile from the Orpheum, where I saw some Broadway shows and a mile and a half from AT&T park to watch a Giants game or two. Great food around Emperor Norton as well- you have to try Pearl's Deluxe Burgers (one block from the Inn).
Overall, this is a great, safe place to stay in the city. I will be visiting SF 4 weeks out of the year and will definitely try to book this room again for those visits. :)