These young philosophers presented a paper on Methodological Naturalism that impressed me enormously. The paper was eventually published in June 2010 [Methodological Naturalism - How Not to Attack Intelligent Design Creationism].
The essence of their paper is that science is not intrinsically limited to methodological naturalism in spite of what many people—especially accommodationists—might say. (And in spite of what was said in court in Dover, Pennsylvania.) Boudry and Blanke (and Johan Braeckman) claim that science is perfectly capable of investigating supernatural claims. However, whenever scientists have done this they have discovered that the claims are either false or unsupported by evidence. Hence, science is characterized by "provisory" methodological naturalism based on empirical evidence. This is very different from "intrinsic" methodological naturalism.
Maarten Boudry has written lots more about pseudoscience in general and Intelligent Design Creationism in particular. It's all published in his thesis: Here Be Dragons. I suggest you read the whole thing!
[Image Credit: rbh.Smaug.jpg. Smaug is from The Hobbit. It's also the favorite dragon of my colleague Craig Smibert who discovered the Smaug (Smg) gene/protein in Drosophila melanogaster.]