I own both a D60 and an S2. (Actually the S2 is my wife's, who has a separate photo business but...) I agree with the first poster that the S2 interpolation is slightly better, but only very marginally. I've commented quite a bit on D60 vs. S2 on the Rob Galbraith forums, my overall conclusion: buy the one that makes you happy.
I think the D60 shoots faster, handles better, and produces the best image quality when the dynamic range is well under control.
I find it easier to get good skintone from the S2, and it seems to have a better dynamic range than the D60, although I haven't tested this rigorously.
How much interpolation you need depends on the medium; I've seen a 40x60 of a bride printed on photo paper with a hybrid printer that was shot with an S1 that looked as good as anything medium format ever did.
Reproduction on press requires more pixels, but I've sent D60 files which I upsampled about 30% (in Photoshop, 5% at a time) look perfect on press at full page size.