This Virtual Special Issue collects the results of six research projects conducted under the umbrella of the MODEX network. MODEX stands for Model Experiments and refers to the combination of qualitative and quantitative model comparisons, the latter based on a harmonized model application. While all projects focused on the comparison of energy system models, the experiments covered a broad range of different areas. Thus, the experiments address different model types, such as vehicle diffusion models, power system models, distribution grid models, and transmission grid models, but also different thematic scopes, such as policy instruments, decentralized flexibility, and sector coupling. In total, the projects involved 40 models. The experiments were based on a harmonization of models and data, which was realized to the degree possible and useful in the respective project context. Complementary to the harmonized model application, the methods and tools for the systematic comparison of energy system models were further developed within the MODEX projects. The results of the MODEX projects significantly expand the spectrum of systematic comparisons of energy system models. The added value compared to previous model experiments consists particularly in the profound characterization of the models involved, the consistent linking of model differences with outcome differences, and the transparent description of appropriate methods and challenges of comparing energy system models. Due to a high degree of transparency, the project findings can be used directly by developers and users of other models.