Effective Field Theories have changed our understanding of Quantum Field Theories. This thesis shows several applications of this powerful tool in the context of the Standard Model and for searches of New Physics. The thesis starts with a review of the Standard Model and its open questions and is followed by an updated and systematic study of models of flavor in the context of Partial Compositeness in Composite Higgs theories. Following that, the question on how to measure the Wilson coefficients of the Standard Model effective operators at present and future experiments is addressed: first by using modern Machine Learning techniques by studying angular distributions for diboson production, followed then by a study on ElectroWeak radiation at a future Muon Collider and how to use it to better probe the new physics parameter space. The fourth chapter deals instead with applying Non-Relativistic Effective Theories to the study of exotic mesons in the Standard Model. The two competing interpretations, a molecule formed of two mesons or a compact tetraquark state, and their consequences are studied. In particular this study is done on the X(3872) exotic charmonium and the consequences of the two accidental tunings of this system are discussed. The last chapter addresses the problem of baryogenesis from the ElectroWeak phase transition. A new scalar sector is introduced that decouples the physics responsible for the generation of the baryon asymmetry from the weak scale. This helps solving the main problems that ElectroWeak baryogenesis models face, namely the large modifications to the Higgs physics and the need of large CP violating new effects.