The Nevsky Hotels are fantastic. Clean, reasonably priced, and about one minute walk from Nevsky prospekt, five-ten minute walk from Church of Spilled Blood, it's great. The Nevsky Aster is where I stayed- there are several, Nevsky Aster, which is more simple, and one across the street from the Aster, which is more business oriented. One thing I liked was that the breakfast at the Aster was really simple and easy, but if you want a great breakfast (with pastries and eggs and blinis and a whole assortment of things) you can eat at the Nevsky Hotel across the street instead for free. There is an internet connection, and it has it's own courtyard, so it isn't right on the street, and it's safe. There's a small grocery store across the street and a two minute walk to the left, and lots of great stuff. Let me knoe if you need more info. It's also really close to the Hermitage.
PS- The Nevsky Hotel group also has a cheaper hotel that is really more like a hostel, much less expensive, but I've never been inside, so I don't know how it compares.
http://www.nevskyhotels.com/