We test several ultrasoft pseudopotentials (US-PPs) and projector augmented-wave (PAW) data sets, calculating the bond lengths, the atomization energies and the frequencies of the vibrational stretch modes of various diatomic molecules. The US-PPs and the PAW data sets are constructed with the same recipe and using the local density approximation or the Perdew, Burke and Ernzerhof generalized gradient approximation for the exchange and correlation energies. We study the dimers H(2), N(2), O(2), F(2), Al(2), Si(2), P(2), S(2) and Cl(2) and several monohydrides, carbides, nitrides and oxides of boron, carbon, nitrogen, oxygen, fluorine, aluminum, silicon, phosphorus, sulfur, chlorine, iron and nickel. We find that US-PPs and PAW data sets constructed with the same parameters provide almost equivalent results for the bond lengths and the vibrational stretch frequencies while, for some molecules, the PAW method is superior to the US-PP method for the calculation of the atomization energies. Our geometries and vibrational frequencies are compared with the results present in the literature and obtained by localized basis sets. It is found that the agreement is very good, with discrepancies comparable to those due to the use of different localized basis sets.