For a strongly regular graph, there are exactly 3 eigenvalues, all nonzero (I believe). One has multiplicity 1, which means the other two have pretty high multiplicities. There are tables that give these eigenvalues and multiplicities:
http://www.win.tue.nl/~aeb/graphs/srg/srgtab1-50.html
For example, the Schlaefli graph is order 27 but has an eigenvalue of order 20.
My question is, are there other known graphs (families, types, or just single graphs) that have large multiplicities of eigenvalues? When I check a random graph in Sage, it seems the max multiplicity is mostly 1.
One class of examples are distance-regular graphs; strongly regular graphs are (essentially) distance-regular graphs with diameter. Distance-regular graphs can be constructed from Hadamard matrices, symmetric designs and linear codes.
If all eigenvalues of the adjacency matrix $A$ of a graph are simple, then any matrix $P$ that commutes with $A$ must be a polynomial in $A$. It follows from this that all automorphisms have order dividing two, and also that the graph either is the complete graph $K_2$ or cannot be vertex transitive So any vertex-transitive on more than two vertices has an eigenvalue which is not simple.
You can learn about these things in Biggs's ``Algebraic Graph Theory'', for example.