the Bra and Ket notation of quantum mechanics uses matrices and matrix operations extensively. Eigenvalues have significance of a system's state in energy levels and there are all kinds of other linear algebra concepts used in things like commutators and applying a hamiltonian to a system. Most importantly is that all of the rules of how these physical properties interact obey the linear algebra theorems.
Another application is in solid-state physics in describing crystal formations, and calculating distance and angles of atoms within a crystal. A crystal can be thought of as a 3D matrix of atoms.
State space descriptions of physical systems are usually kept in matrix form.
I haven't looked into this too much, but matrices are also applied in all kinds of mathematical transforms like the Fourier transform which is used in physics to describe frequency spectrums.
Ray tracing, which attempts to represent EM, acoustic, etc. waves as discrete rays, is often done as matrix operations, because a new ray is basically a translation and angle transform of its previous ray.
Then there are many other applications of matrices in engineering and computer science.