We study the noise correlations of one-dimensional binary Bose mixtures, as a probe of their quantum phases. In previous work [Phys. Rev. A 80, 023619 (2009)], we found a rich structure of many-body phases in such mixtures, such as paired and counterflow superfluidity. Here we investigate the signature of these phases in the noise correlations of the atomic cloud after time-of-flight expansion, using both Luttinger liquid theory and the time-evolving block decimation (TEBD) method. We find that paired and counterflow superfluidity exhibit distinctive features in the noise spectra. We treat both extended and inhomogeneous systems, and our numerical work shows that the essential physics of the extended systems is present in the trapped-atom systems of current experimental interest. For paired and counterflow superfluid phases, we suggest methods for extracting Luttinger parameters from noise correlation spectroscopy.