There is a good list of guesthouses here.

Ganpati Guesthouse: . Photo Sphere: Click here.

Groovy Ganges Guesthouse: Assi Ghat, Varanasi. Website: website here.
Attracts long-term visitors (like me in the coming years, perhaps!) and students doing research projects in Varanasi. If you stay more than three weeks, you could get a room with a/c for 500 Rupees per night. You could get Hindi, Sanskrit and Astrology classes right in your room with a well experienced private tutor. Groovy Ganges also rents out apartments next to the property.

Kumiko House: .

Monu Family Paying Guest House: . Website: website here.

Very colorful place, as the video above will demonstrate. Single room with fan for 300 Rupees (and that is a 2011 price).

Om Guest House: Near Ganga River. Website: website here.
Rooms with commode inside from 150 Rupees.

Puja Guesthouse .

Scindhia Guest House: Overlooking the Ganges, Varanasi. Website: website here.
A room with shared bath and window looking down on to the Ganges goes for 400 Rupees a night.

Tiwari Lodge: . Website: website here.
Said someone on India Mike: "A very good source of information for me, and a great and kind and information-filled man, is Raju - who owns and runs the Tiwari Lodge, across from the Haifa on the road to Asi. I stayed at the Tiwari for six months during my last stay and he never failed to find the people I needed when I needed them."

Yogi Lodge: .
Legendary place.