Hotel Chuo Selene / Hotel Kinki for Osaka.
Or Super Hotel near Shin-Osaka station too.
Tokyo, well, try 1 of the Toyoko-inn.
Or check rates for hotels near Ueno station or Ikebukuro station perhaps?
Kyoto, well, u either have to book the hotels early and for off-peak season if you want a good price. Sometimes I can get 1 of the hotels near Kyoto station for between S$100-110 per night.
But if it's during peak seasons (Spring/Autumn), then most hotel's rates will go up. If you don't mind not having your own private toilet, then maybe consider Piece Hostel Kyoto, near Kyoto station? I've stayed there before and it was decent for the price.