In this paper we make an SL(2,Bbb Z)-covariant generalisation of the noncommutative theories, NCYM and NCOS on the D3-brane, and NCOS on the D5-brane in type IIB. Usually, the noncommutative theories are obtained by studying perturbative F-string theory, and the parameters governing the noncommutative theories are given by the open string data. The S-duality of NCYM and NCOS on the D3-brane has been seen by dualising the background, keeping the F-string theory under study fixed. We give an SL(2,Bbb Z)-covariant generalisation of the open string data relevant when one instead studies perturbative (p,q)-string theory. The S-duality of NCYM and NCOS on the D3-brane is reproduced by instead keeping the background fixed and studying different (p,q)-string theories. We also obtain new noncommutative open (p,q)-string theories on the D3-brane and the D5-brane which are S-dual to ordinary NCOS. The theories are studied using the supergravity duals of the D3-brane and the D5-brane, corresponding to a probe brane in the relevant background.