I've read three of his books and disagree with some of his views on philosophy: blaming Thomas Aquinas for separating nature and grace and thereby making way for the Enlightenment seems like an enormous exaggeration. There were plenty of philosophers during that time period more guilty of presaging modernism than Aquinas. Why not blame everything on William of Ockham, the Franciscan who stole some horses and ran away?
I think Schaeffer's greater contribution was his ability to communicate with both Christians and non-Christians, encouraging them to ask serious questions about truth. He helped people from both groups realize that Christianity didn't have to be intellectually lightweight. In my book, his most important impact was achieved more on a personal than a theoretical level.
He was also willing to treat waste and pollution of the environment as a serious theological issue before doing that became cool. He wrote a book on the topic; I haven't read it yet, but I'd like to.