I've written a book on the foundations of perturbative quantum field theory, from a point of view which emphasizes the Wilsonian low-energy effective field theories. The book can be downloaded as one file, or chapter by chapter:

(Last update: 22 October 2009).

I also have some slides from talks I've been giving about this material.

Renormalization and the Batalin-Vilkovisky formalism arXiv:0706.1533  This paper contains an early version of some of the ideas in the longer paper above.  The aim of this paper was to get, as quickly as possible, to the construction of a non-trivial theory (perturbative Chern-Simons theory).  Unfortunately, though, this paper doesn't do a good job of explaining the Wilsonian philosophy underlying everything, so I wouldn't really recommend reading it.