Microfluidics refers to the interdisciplinary technology that deals with handling and processing small amounts of fluids in channels with micrometre-scale dimensions. This technology has arisen as an influential experimental and research platform that presents manifold advantages to diverse fields, including medicine, science, and engineering. Among the various microfluidic subcategories, droplet-based microfluidics has gained significant traction in commercial settings. However, despite this success, several significant challenges remain, including a limited understanding of the underlying physics and mechanisms, complex interactions, device instability, the necessity of surfactants, multiple effective parameters, and a high level of expertise required to operate microfluidic hardware. These challenges have restricted the advancement and utilization of droplet-based microfluidics in further applications. The present thesis mainly focuses on enhancing our comprehension of droplet generation while developing a new application for droplet-based microfluidics. This thesis aims to achieve the following research objectives: (1) designing and fabricating reliable and stable microfluidic devices for generating core-shell droplets, (2) investigating the fundamental physical factors contributing to droplet generation, (3) evaluating the thermal and mechanical endurance of core-shell particles through theoretical and experimental methods, and (4) exploring the potential use of core-shell particles in a digital polymerase chain reaction (PCR). [...]