We study the minimum number of distinct eigenvalues over a collection of matrices associated with a graph. Lower bounds are derived based on the existence or non-existence of certain cycle(s) in a graph. A key result proves that every Johnson graph has a signed variant with exactly two distinct eigenvalues. We also explore applications to weighing matrices, linear ternary codes, tight frames, and compute the minimum rank of Johnson graphs. Further results involve the minimum number of distinct eigenvalues for graphs in association schemes, distance-regular graphs, and Hamming graphs. We also draw some connections with simplicial complexes and higher-order Laplacians.