In Manali my vote would go to hotel Kalinga, stayed there twice in 2004 in off season and the room rent was Rs. 500 for a double bedroom room with bath tub etc.
For budget travelers in Manali hotel Shingar is also ok, you get double bed room with attached toilet, tv, round the clock hot water for Rs. 150 a night in off season.
Can't say about Leh because I had stayed in government guest house, but near Pangong Tso the Eco huts at Rs. 250 a night are really good. For Kargil, Drass, Rangdum and Padum (Zanskar) the J&K tourist bungalow are the best with low tarifs and good accommodation.