There are different types of critiques of Christianity. Each one of them stresses something different coming from different areas of expertise. Some of the major areas of criticism come from 1) The sciences, especially evolution and brain science; 2) Biblical and historical criticism; 3) Philosophy, especially the philosophy of religion; 4) Archaeology; 5) Cultural anthropology; 6) Psychology; and, 7) Social and moral criticism of the Bible and the church. There are others. What atheists think is a more effective criticism is not always the same as what Christians think is more effective.
I suspect we won't all agree. Without the sciences (#1) we probably don't have much of a critique at all, at least no reasonable alternative to a creator God, so that has got to be the highest on the list. But here's the problem. Christians denigrate the sciences in favor of their holy book. In every era Christian believers have repeatedly said that reason must bow down before faith, you see. That's the problem when using the sciences in getting Christian believers to change their minds. We must first help believers see that their holy book has holes in it. To do that we must speak to them in their language by critiquing their beliefs in terms they will understand and appreciate. Otherwise we're preaching to the choir.
Sometimes John Loftus says things that make a lot of sense. Often it seems he gives with one-hand (the first paragraph) and takes away with two (the second paragraph). Science really does not provide any evidence or facts that require one to come into conflict with anything in the Bible. Atheist usually choose to see evolution and Genesis as by necessity being in conflict. This isn't true. The Bible gives us no information that disagrees with the age and timescales arrived at through science. Nor does the Bible gives any alternate timeline. As for macro evolution - all living things having a single common ancestor, neither the Bible or Science support that conclusion no matter how many transitional fossils they think they find. DNA Evidence doesn't work either because there hasn't been an example of a positive mutation that resulted from a gain of information - only loss. Loftus has been trying to validate that there is something wrong with the Bible instead of himself. This isn't the case. The problem is us. Not God. We know the correct standard by which we should live but either cannot or refuse to accept those standards. Being a Christian does mean bowing the knee before God and admitting our sin and our inability to reach those standards without His help. If you are unwilling to do that you are not born-again and never has been. Science is not a problem for the Bible, but sin is the problem for us. 3
Debunking Christianity: PZ Myers and the Courtier's Reply Again