See also Experimental design.
Pearl, J. (1995). Causal diagrams for empirical research. Biometrika, 82(4), 669–688. doi:10.1093/biomet/82.4.669
Pearl, J. (2009). Causal inference in statistics: An overview. Statistics Surveys, 3, 96–146. doi:10.1214/09-SS057
General introduction to causal diagrams, confounding criteria, counterfactuals, and so on.
Scott Cunningham’s Causal Inference: The Mixtape, a free causal inference book (though written for Stata). Includes discussion of matching, regression discontinuity, instrumental variables, differences-and-differences, and other causal designs commonly used in economics.