I suspect that bone can change wildly from sample to sample which gives an advantage to one of the man-made materials for manufacturers to use (consistent tone from instrument to instrument). However, I much prefer a bone saddle and nut to any other material. As Mike already noted, bone seems to have an immediate reaction to string plucking (punch) and also seems to impart a brighter ring or more upper harmonics to string tone (clearer, more crystalline).
I also like that bone allows you to stain it to make it match older instruments (a little brown stain will make the bone look aged). And bone polishes up very nicely to a shiny, smooth finish.