We investigate a two-orbital Hubbard model on a honeycomb structure, with a special focus on the antisymmetric spin-orbit coupling (ASOC) induced by symmetry breaking in the electronic degrees of freedom. By investigating the ground-state phase diagram by the mean-field approximation in addition to the analysis in the strong correlation limit, we obtain a variety of symmetry-broken phases that induce different types of effective ASOCs by breaking of spatial inversion symmetry. We find several unusual properties emergent from the ASOCs, such as a linear magnetoelectric effect in a spin-orbital ordered phase at 1/4 filling and a spin splitting in the band structure in charge ordered phases at 1/4 and 1/2 fillings. We also show that a staggered potential on the honeycomb structure leads to another type of ASOC, which gives rise to a valley splitting in the band structure at 1/2 filling. We discuss the experimental relevance of our results to candidate materials including transition metal dichalcogenides and trichalcogenides.