This paper provides a comprehensive review of hybrid energy systems (HESs), focusing on their challenges, optimization techniques, and control strategies to enhance performance, reliability, and sustainability across various applications, such as microgrids (MGs), commercial buildings, healthcare facilities, and cruise ships. The integration of renewable energy sources (RESs), including solar photovoltaics (PVs), with enabling technologies such as fuel cells (FCs), batteries (BTs), and energy storage systems (ESSs) plays a critical role in improving energy management, reducing emissions, and increasing economic viability. This review highlights advancements in multi-objective optimization techniques, real-time energy management, and sophisticated control strategies that have significantly contributed to reducing fuel consumption, operational costs, and environmental impact. However, key challenges remain, including the scalability of optimization techniques, sensitivity to system parameter variations, and limited incorporation of user behavior, grid dynamics, and life cycle carbon emissions. The review underlines the need for robust, adaptable control strategies capable of accommodating rapidly changing energy environments, as well as the importance of life cycle assessments to ensure the long-term sustainability of RES technologies. Future research directions emphasize the integration of variable RESs, advanced scheduling, and the application of emerging technologies such as artificial intelligence and blockchain to improve system resilience and efficiency. This paper introduces a novel classification framework, distinct from existing taxonomies, addressing gaps in prior reviews by incorporating emerging technologies and focusing on the dynamic nature of energy management in hybrid systems. It also advocates for bridging the gap between theoretical advancements and real-world implementation to promote the development of more sustainable and reliable HESs.