This thesis presents some recent developments in the study of Generalised Clifford Algebras, their associated structures, and their physical applications. The investigations are extensions of L-Matrix theory with Grammer of Dirac Matrices, and their generalisations. Commutation Matrices, Product Transforms are some of the new concepts introduced in this thesis. Generelasation of the 'Matrix Decomposition Theorem', Canonical transformations in Quantum mechanics, Formulation of 'Generalised Clifford Groups' are some of the main and new concepts focused in this thesis. Further, a complete, simple and explicit solution to the problem of projective representations of finite abelian groups is discussed in the thesis. This study proposes a negative energy relativistic wave equation, as a counter part of Dirac's positive energy relativistic wave equation. Commuting Quartenion algebras of Clifford and L-Matrix Theory, Resevski's approach to Clifford algebras, with its generalisation are discussed in this thesis.