Even for these 2 obsolete cameras, they are worlds apart. One is a professional-grade DSLR, then other is more "prosumer". In the used market, prices will probably differ quite greatly too. Kinda had/unfair to make comparison like that.
The build quality of the D1 greatly outclass that of the S1 Pro. Picture quality - subjective. The D1 also has a much higher performance (AF speed, continuous shooting speed, CF writing speed etc) as well. What the S1 has is probably the (many said) excellent out-of-camera images.