There is one argument regarding free will which seems to come up time and time again, and it deserves a response. There was the week before last Sunday School linked blog making it, and the blog in the title. The basic argument is that since our brains are made of physical matter/particles/molecules/etc, and therefore play by the rules of chemistry/physics, there can be no free will since these tend to be deterministic. Unfortunately, it's a not a very good argument, and I will dare the next person making it to run their brain through a meat grinder. Hey, nothing's lost, right? :)
The error in the argument is the underlying assumption that nothing can be more than the mere sum of it's parts - the body is molecules, molecules are physics, the body is physics (gross oversimplification of the argument, I know). However, this is akin to saying that the Brazilian rainforest is a collection of trees, L'Étranger is letters on paper, the Internet is TCP/IP, or the Dance of the Knights is sound waves; Technically all those statements are correct. But all of those things are clearly more in aggregate than the individual components which make them up, you simply cannot get the sum from adding bottom up. On the other hand, if you take a top down approach it's quite clear that as you start subtracting one unit, more than one unit is lost from the total, and the same applies to organic life. The best illustration of the principle is probably the network effect.
That is not to say that our brain is capable of some sort of metaphysical activity per se (nor that there aren't good arguments against free will), only that the physical sciences may not be best tool for analyzing whether or not we are able to make non-determined/free willed choices. My feeling is that attempting to answer questions of 'why' with the answers of 'what' is misguided. We are products of nature with certain emergent properties, and free will may be the result of our conscious self awareness.