We theoretically investigate Josephson junctions with a phase shift of π in various proximity induced one-dimensional superconductor models. One of the salient experimental signatures of topological superconductors, namely the fractionalized 4π periodic Josephson effect, is closely related to the occurrence of a characteristic zero energy bound state in such junctions. We make a detailed analysis of a more general type of π-junctions coined 'phase winding junctions' where the phase of the order parameter rotates by an angle π while its absolute value is kept finite. Such junctions have different properties, also from a topological viewpoint, and there are no protected zero energy modes. We compare the phenomenology of such junctions in topological (p-wave) and trivial (s-wave) superconducting wires, and briefly discuss possible experimental probes. Furthermore, we propose a topological field theory that gives a minimal description of a wire with defects corresponding to π-junctions. This effective theory is a one-dimensional version of similar theories describing Majorana bound states in half-vortices of two-dimensional topological superconductors.