This review synthesizes recent advances on alternative fuels for Homogeneous Charge Compression Ignition (HCCI) engines, focusing on biomass-derived blends (e.g., biodiesel, ethanol/butanol mixtures) and hydrogen. HCCI combines the high thermal efficiency of compression ignition with the ultra-low NOx and soot potential of premixed, low-temperature combustion. Biofuels, owing to their inherent oxygen content, generally suppress smoke and NOx but can elevate CO/HC under certain volatility and oxidation constraints; blend composition strongly influences auto-ignition phasing and load range. Hydrogen, with fast kinetics and wide flammability limits, extends stable lean operation and reduces carbon at the tailpipe, yet poses challenges in volumetric efficiency, power density, and combustion control. This paper consolidates evidence on mixture preparation, ignition timing management, and emissions trade-offs, and highlights solutions such as multi-fuel blending, intake heating/boost, variable valve strategies, EGR, and spark-assisted compression ignition to widen the feasible operating map. Future work should co-optimize fuel chemistry and closed-loop control for robust, clean, and efficient HCCI.