"Antonio House" hostel
http://www.antoniohouse.ru/
http://www.minihotelspb.ru/minihotel_74_77.html
Located in the very center (500 m from Nevsky Prospekt, 15 minutes walk from Moskovsky and Vitebsky Rail Terminals).
See location on Google Maps.
Prices from $12, very good conditions. I recommend!
Other hostels
http://www.ap-tour.ru/hostel-petersburg.htm
http://www.russia-hostelling.ru/rus/hostels.php