I can highly recommend the Linos Inn in Kakopetria, north of Troodos square (on the B9 road). It's situated in the old quarter of Kakopetria - the word "kakopetria" means "ugly stone" and this hotel is on a cobbled stone street with tons of charm and character.
The hotel is not the cheapest in the Troodos but it is warm and cosy, rooms have antique furniture and four poster beds and underfloor heating (great in the winter months). The hotel is a series of renovated houses with wooden beams and old fashioned mud/straw bricks
It is very popular so book early to make sure of a room.