The Relevance of the Two-Sector Production Model in Trade Theory, Jones and Sheinkman .
A great article on the Core. This is an important welfare economics and cooperative game theory concept that we would cover if we had time.
Cowles Commission Monographs: These are some of the great research monographs in the early history of modernn economic theory. These texts are classic, full of insight, and accessible. Take a look.
Hood and Koopmans, ed., Studies in Econometric Method. Theory is interesting only to the extent that it helps us to organize data. Several papers in this volume are foundation papers for contemporary econometrics. I particularly recommend Marschak's paper, chapter 1, which discusses what it could mean for a model to be "structural".
Gerard Debreu, Theory of Value. Everyone with a serious interest in general equilibrium and its applications should read this book.
Notes on correspondences. These notes are by Kim Border. They are advanced, but very clear. Kim has other notes on his web page that you might find useful.
The von Neumann expanding economy model has many intereting applications, including the modelling of metabolic networks in cells. Particularly interesting is the idea of a statistical mechanics of von Neumann models.
I don't think it is a good idea to write a thesis in decision theory, but if you have interests in this area, you will want to look at Peter Wakker's bibliography, a superb source for the literature.
What I think Theorists Should be Doing
Some thoughts on general equilibrium theory and welfare economics from an interview at the University of Chicago.