We study the quantum phases of mixtures of ultracold bosonic atoms held in an optical lattice that confines motion or hopping to one spatial dimension. The phases are found by using the Tomonaga-Luttinger liquid theory as well as the numerical method of time-evolving block decimation (TEBD). We consider a binary mixture of equal density with repulsive intraspecies interactions and either repulsive or attractive interspecies interaction. For a homogeneous system, we find paired and counterflow superfluid phases at different filling and hopping energies. We also predict parameter regions in which these types of superfluid order coexist with charge-density wave order. We show that the Tomonaga-Luttinger liquid theory and the TEBD qualitatively agree on the location of the phase boundary to superfluidity. We then describe how these phases are modified and can be detected when an additional harmonic trap is present. In particular, we show how experimentally measurable quantities, such as time-of-flight images and the structure factor, can be used to distinguish the quantum phases. Finally, we suggest applying a Feshbach ramp to detect the paired superfluid state and a pi/2 pulse followed by Bragg spectroscopy to detect the counterflow superfluid phase.