This dissertation studies aspects of three of the biggest unsolved problems with the Standard Model of Particle Physics: the matter-antimatter asymmetry in the universe, neutrino masses, and dark matter. While the SM has been very successful in explaining most experimental results, it does not provide a satisfactory solution to the matter -- anti-matter asymmetry problem. One of the simplest and most elegant solutions to this problem is electroweak baryogenesis. An addition to the Standard Model of a real, gauge-singlet scalar field, coupled via a Higgs portal interaction, can reopen the possibility of a strongly first-order electroweak phase transition and successful electroweak baryogenesis. In the first part of this work, we study a subset of such models and evaluate the bubble nucleation temperature throughout the parameter space where a first-order transition is expected. In addition, we also look at vacuum bubble wall velocity and how it impacts baryogenesis in these models. Another limitation of the SM is that it models the neutrinos as massless, even though experiments have shown that this is not true. The mass generation mechanism of neutrinos is still unknown, and popular see-saw models with Majorana masses have proven difficult to test. The Clockwork mechanism can be used to generate Dirac masses, and can explain the smallness of neutrino masses without introducing unnaturally small input parameters. In the second part of this thesis, we study the simplest Clockwork neutrino model, the "uniform" clockwork, as well as a broader class of "generalized" clockwork models. We derive constraints on such models from lepton-flavor violating processes, as well as precision electroweak fits. Further, we analyse simulated collider data and study the prospects for detection of the models at the LHC and future colliders. The third and final part of this thesis is about Dark Matter. All the evidence we have for Dark Matter (DM) is through gravitational interactions, and its microscopic nature is one of the most urgent questions in theoretical physics. We present an unconventional model for the production of dark matter: the conformal freeze-in scenario. At the time when the dark sector is populated in the early universe, it is described by a strongly coupled conformal field theory and as such, cannot be described by particle states. As the universe cools, cosmological phase transitions in the standard model sector or loop induced deformations of the conformal field theory induce conformal symmetry breaking and confinement in the dark sector. One of the resulting dark bound states is stable on the cosmological time scales and plays the role of dark matter.