Buchanan, James, What Should Economists Do?

Cairnes, John Elliot, The Character and Logical Method of Political Economy

This tautly reasoned work begins by comparing the logical and scientific methods of various sciences (such as physics and chemistry) with the logical and scientific methods available to economists. Cairnes then illustrates the power of working out those principles by examining debates of the early to middle 1800s. He devotes a chapter each to clear expositions of Malthus's population principle (Lecture VII) and Ricardo's development of the theory of rent (Lecture VIII). His discussions set a new standard of careful thinking about economics. Cairnes's explanations are written with unusual clarity, making this book a great way to learn to think clearly about economics proposals in general, whether they are presented as loosely as in the popular press or as precisely as in advanced research papers.

Klamer, Arjo and David Colander, The Making of an Economist

Klein, Daniel, (ed.), What Do Economists Contribute?

Knight, Frank, On the History and Method of Economics

McCloskey, Donald, If You're So Smart: The Narrative of Economic Expertise

McCloskey, Donald, Knowledge and Persuasion in Economics

McCloskey, Donald, The Rhetoric of Economics

Mill, John Stuart, Essays on Some Unsettled Questions of Political Economy (originally published 1844; reprinted 1874 with minor spelling modernizations)

John Stuart Mill's Essay V in Some Unsettled Questions of Political Economy contrasts induction and deduction in political economy, a science with limited ability to run controlled experiments. Almost 75 years later, in the light of burgeoning developments in mathematical logic and statistics, Jacob Viner of the University of Chicago took Mill on, in his "Some Problems of Logical Method in Political Economy." The two essays create an exciting counterpoint, sure to make you think.

Also of interest:

Subjectivist methodology: selected quotes and bibliographical references by N. Barry, J. Shearmur, D. Gordon, and J. N. Gray from various Literature of Liberty essays on spontaneous order, C. Menger, and F. A. Hayek.
"Vernon Smith, Economic Experiments, and the Visible Hand," by Don Coursey

Mill's book contains several other essays of interest. I recommend Essay I, containing an outstanding, succinct summary of comparative advantage. In it, Mill raises the interesting question: "Who gains the most from trade?" That question persisted into the work of Walras, Pareto, Edgeworth, Samuelson, and many others who subsequently clarified marginal utility, indifference curves, social welfare, and the distribution of wealth.

Morgenstern, Oskar, On the Accuracy of Economic Observations

Robbins, Lionel, The Nature and Significance of Economic Science

Whately, Richard, Introductory Lectures on Political Economy

Archbishop of Dublin and Professor of Political Economy at Oxford, Richard Whately first gave this series of lectures in 1831. Described (perhaps by his students) as a "preface to a preface," the book delves with wit and clarity into the philosophical foundations of economics. One of Whately's goals is to demonstrate that economics is morally consistent with Christianity, and that the human motive toward self-improvement—including the acquisition of wealth—is God-given. But make no mistake: this book is not primarily about religion, but about economics. Whately wittily addresses many of the same specious objections to economic thought addressed by professors today in speaking to their classes about common errors made by laymen. This is also the book in which Whately famously proposed the word "catallactics", or the 'Science of Exchange,' instead of the term 'political economy.' Pertinent to that, see Lecture IX, in which he discusses the consequences of any choice of new scientific terms and the consequences of unclear definitions.