The eigenvectors of a matrix form a complete orthogonal basis if and only if the matrix commutes with its Hermitian conjugate (i.e. the complex conjugate of its transpose). Matrices with this property are called "normal". Any Hamiltonian is Hermitian: it is equal to its Hermitian conjugate. Any quantum time evolution operator is unitary: its Hermitian conjugate is its inverse. Any matrix commutes with itself and its inverse, so the eigenvectors of any Hamiltonian or time evolution operator will always form a complete orthogonal basis. (I don't remember what the answer is if you don't require the basis to be orthogonal.)