Peter A. Hall, “Aligning ontology and methodology in comparative politics”, in James Mahoney and Dietrich Rueschemeyer (eds.) Comparative Historical Analysis in the Social Sciences (2003), Chapter 11.

Summary: Hall advances a reconceptualisation of the comparative method, realigning the roles of ontology and methodology in comparative politics. Hall argues for the importance of methodologies being congruent with prevailing ontologies. The author argues that small-N research designs based on systematic process analysis has the potential to resolve the ontology/methodology divide, especially since they provide a way to assess causal theories.
Method: Similar to Laitin, Hall establishes a theoretical framework to qualitatively explain the trajectory of the comparative method to this point; in this case, he looks uses thick description of some of the more prevalent methodologies in the field from historical institutionalism, to behaviouralism and structural-functionalism.
Important Insight: A notable point in this article is Hall’s illustration that the ontological shifts in the comparative field have not been unidirectional; rather, there is increased questioning of causal explanations and a renewed emphasis on historical explanations that take into account multiple streams of causation and endogeneity in causal arguments.
Critique: Hall’s argument could be further refined by addressing the ontology/epistemology debate, which is perhaps a bit more nuanced than simply the methodological/ontological debate. Indeed, these terms should be discussed not at the exclusion of the understanding of epistemology as a part of the larger comparative method discussion.
Note: This article has a great overview of the history of the comparative method.