Category theory is supposed to be one such tool, even though some find it very abstract. It's very much in the spirit of finding analogies among theories and analogies among analogies. (I swear I'm not trolling :P) I'm still working on my understanding of category theory, but somebody who has the mathematical fortitude might enjoy: http://groupoids.org.uk/pdffiles/Analogy-and-Comparison.pdf

In general better abstractions(similar ideas as in a recent discussion of Peter Naur's "Programming as theory building").