  In this paper we resolve the complexity of the isomorphism problem on all but
finitely many of the graph classes characterized by two forbidden induced
subgraphs. To this end we develop new techniques applicable for the structural
and algorithmic analysis of graphs. First, we develop a methodology to show
isomorphism completeness of the isomorphism problem on graph classes by
providing a general framework unifying various reduction techniques. Second, we
generalize the concept of the modular decomposition to colored graphs, allowing
for non-standard decompositions. We show that, given a suitable decomposition
functor, the graph isomorphism problem reduces to checking isomorphism of
colored prime graphs. Third, we extend the techniques of bounded color valence
and hypergraph isomorphism on hypergraphs of bounded color size as follows. We
say a colored graph has generalized color valence at most k if, after removing
all vertices in color classes of size at most k, for each color class C every
vertex has at most k neighbors in C or at most k non-neighbors in C. We show
that isomorphism of graphs of bounded generalized color valence can be solved
in polynomial time.
