Superstitious religious practices are those that claim a quid pro quo relationship with the divine. This may be seen in practices like burying a St. Joseph statue in the yard of a house you want to sell or simply showing up in church on Christmas and Easter to "cover your bases." Whether it is charismatic theology demanding the gift of tongues or health and wealth "name-it-and-claim-it" theology, we are practicing sorcery when we claim to so manipulate God. This creates a god who is either petty or weak. It is definitely creating gods in our own images and thus the atheists can easily dismiss this type of religion.
Fundamentalists of various stripes make truth claims that don't hold up to reason. The obvious current example is creationism (even disguised as intelligent design). This is a religious tenet when presented as young earth thinking or simply a philosophy when it doesn't rely on Biblical assertions. In either case it is not bad science, it is simply not science. That's ok as long as it doesn't pretend to be science, but sadly it does. Since the atheists are touting reason and the scientific method there is no room for discussion here.
Perhaps the greatest fuel for the fire of the current tendency to reject God is the way that so many religious folks claim exclusivity based on what they perceive to be ultimate reality revealed through a very particular tradition. These sorts of claims are not limited to fundamentalists. In Christianity, it is not only the Evangelicals and Orthodox believers who make this claim, but most of mainline Protestantism and nearly all of Catholicism claims that Jesus is the sole provider of salvation. Consider how this appears to the objective viewer. This claim of exclusivity has been at the heart of all the religious bloodshed throughout history. This is the reason that churches and individual believers have been able to act in ways completely counter to the teachings of the traditions they teach. This is handing the loaded gun to our detractors while it is still smoking from shooting ourselves in the foot!
So what would I say to the new atheists? Glad you asked ;-) My first challenge to them would be to prove what they claim, i.e. that there is no God. I'll concede that I cannot prove the existence of God, that is something that I take on faith for very personal reasons. But, there is also no proof that God doesn't exist and so that can only leave us all with some form of agnosticism, which literally means a lack of knowledge. I don't know that God exists, but I choose to believe that God does. The atheists likewise don't know, but they choose to believe that God doesn't exist. In either case we are agnostics with biases, some of us toward God and others away.
My next statement to the atheists would be to assure them that I also don't believe in the god they don't believe in. My journey of faith has taken me away from that place where I accepted that ultimate and objective truth had been handed down to me through the Bible. I now realize that that belief was simply a choice to believe what others taught. I now choose to believe that the Bible is a human document that charts our striving toward God, not God's vehicle to dictate doctrine to us. It is in this journeying, seeking, not knowing, but choosing to believe that I think I may share some common ground with the new atheists.
The new atheists are skeptics, testing hypotheses by employing the scientific method. If something doesn't stand the scrutiny of skeptical thought then it must be rejected and replaced with something that does. Frankly, I can embrace this methodology for my spiritual pilgrimage. I don't have a need for answers. I realize that ultimate truth is something that my finite mind is not capable of grasping completely. So instead I choose to look for truth in the present moment, appropriating it to where I am at this point, not trying to lay claim to the totality of the picture. So I am not afraid to ask tough questions, if God can't handle my questions, then God isn't God! My faith journey thus resembles a scientific inquiry. I form a hypothesis, such as God is love, and then I test it. In the course of this questioning I discover evidence to support the hypothesis and incorporate what I learn to deepen my faith, thus guiding me to further questioning.
Truth be told, I'm pretty certain that most religious people are this sort of seeker most of the time. It's just that we have bought the methodology of the catechism and subject ourselves to the tyranny of answers instead of the liberation of questions. We find it easier to retreat to dogma and fight to maintain integrity and purity of orthodox declarations. This is what fires up the rationalists to debunk what they see as destructive religion. And in this case they are right.
The problem I have with the atheists is that they don't have room in their thinking for something that can't be proven but might still be worth believing. I choose to believe that God exists because that is how I make meaning and learn to live a life that values the other. Atheists find other ways to do the same thing. I think there is something important to be learned from each other if we can stop sniping at each other long enough to listen.