General Issues:
Why Some People Simply Will Not Be Convinced
“My Genes Made Me Do It”: Is Ethics Based on Biological Evolution?
Four Quotes On Natural Selection by Naturalists That Support Theism
Four Problems in Atheist/Theist Discussions
The Most Common Objection on a College Campus
A Look at God’s Existence: Evidence We Want vs Evidence We Should Expect
Blinded by Scientism, by Edward Feser
Why Science Needs Metaphysics by Robin Trigg
30 Suggested Readings on Apologetic Responses to Atheism/Skepticism
Why Are There So Many Atheists on College Campuses
Frank Turek On Why People Reject God
What Can We Know? Epistemology 101 and Religious Belief
New Atheism and the Scientistic Turn in the Atheism Movement by MASSIMO PIGLIUCCI
God, Science & the Big Questions: Leading Christian Thinkers Respond to the New Atheism
It’s Easy to Disprove the Existence of God
Why No One Believes Atheism/Naturalism is True
A Response to the Friendly Atheist (Part 1) by Robin Schumacher
Dr. Kelly Clark – Is Atheism ‘Normal’? Reflections from the Cognitive Science of Religion
Does Science Prove That God Does Not Exist? A Look at Richard Dawkins
Peter Kreeft on God or Atheism — Which Is More Rational?
Challenging Atheism’s Definition of Faith
The Myth That the Bible is Just a Myth by by Robin Schumacher
Why Do You Believe in God in the Absence of Good Arguments?
Old Answers to the New Atheism: An Interview with Peter Hitchens
What Would Change Your Mind about Christianity?
How to Consider the Evidence for Theism by David Glass
Atheism and the Burden of Proof by Paul Copan
If God wanted us to believe in him, why doesn’t he give us more evidence?
Resources on Atheism and the Relationship Between Science and Religion
Frank Turek/David Silverman Debate on What Explains Reality Better-Theism or Atheism?
Historical skepticism:
“I am not sure if Jesus existed”
“ The New Testament authors are biased”
“ We can’t know much of anything in history”
“ History is always written by the winners”
“Jesus’ Followers Fabricated the Stories and Sayings of Jesus”
“The New Testament story of Jesus was borrowed from paganism/mystery religions!
“ There are books that are supposed to be in the Bible that were kept out. Hence, we can’t trust the books we do have in the Bible.”
“The Bible has been translated over and over. We can’t trust it”
Resources:
Historical Epistemology: Resources on The Historical Jesus
Is Jesus Just a Retelling of Mythology: Articles by Jim Wallace
What Can Paul Tell Us About Jesus?
“Jesus’ Followers Fabricated the Stories and Sayings of Jesus”
An Interview with Daniel B. Wallace on the New Testament Manuscripts
Bart Ehrman Creates Stir in Atheist Community Over The Existence of Jesus
Josephus and Jesus. By Paul L. Maier, The
Russell H. Seibert Professor of Ancient History,
Biblical Archaeology: Factual Evidence to Support the Historicity of the Bible
Bart Ehrman On Why There Are Jesus Mythers
The Lack of Unbiased Evidence for Jesus
From Jesus to Us: A Look at P.O.W.E.R.
The Gospels as Historical Biography (Richard Bauckham)
Was Early Christianity Corrupted by ‘Hellenism’?
Was Jesus Christ just a CopyCat Savior Myth? Glen Miller
Who wrote the Gospels? Dr. Timothy McGrew
Did Jesus Even Exist?-The Problematic Argument from Silence
84 Confirmed Facts in the Last 16 Chapters of the Book of Acts
59 Confirmed or Historically Probable Facts in the Gospel of John
Skepticism about the Bible and issues of Interpretation:
“I don’t think we can take the Bible literally”
“ I cant accept Genesis if it says the earth is only 6,000 years old”
“ You can’t expect me to accept a book that condones the killing of innocent people (i.e. the Canaanites, etc)”
“ Why does the Bible condone slavery?”
“Why does the Bible say women are supposed to be in submission to men?”
“How can you accept a book as an authority when it says homosexuality is wrong?”
Resources:
What Happens When Atheists Don’t Care About Hermeneutics?
Dr. D.A. Carson on 12 Principles of Biblical Interpretation …
Killing the Canaanites: A Response to the New Atheism’s “Divine Genocide” Claims By Clay Jones
9/11: Are We All Moral Monsters? by Clay Jones
Does the Old Testament Endorse Slavery? An Overview: Paul Copan
Why Is the New Testament Silent on Slavery — or Is It? By Paul Copan
Evolution and Science/Creation conflict:
“Evolution has shown we don’t need to posit God as an explanation for the complexity of life”
“ Science has a better track record than religion. We keep looking for answers. Your God arguments are science stoppers!”
“Intelligent Design is bad science and not even science at all”
“ Evolution is fact” (never mind that fact that every time someone says this that they don’t even define what evolution is).
Resources:
Sorry; No Such Thing as a Scientific Argument Against the Existence of God
God, Sean Carroll, and the Origin of Nature
The Supposed Warfare Between Christianity and Science
Four ways that the progress of experimental science conflicts with atheism
Has Science Eliminated God? Alister McGrath
Why Is Evolution So Widely Believed? by William Lane Craig
Intelligent Design Is a Historical Science, Just Like Darwinian Evolution
What Are the Top Ten Problems with Darwinian Evolution?
The Evolutionists’ Complaint: It’s Wrong to Argue For ID By Arguing Against Evolution (Part 1 of 3)
God and Evolution: A Healthy Debate
John Lennox: God’s Undertaker – Has science buried God?
Is Science a Threat or Help to Faith?
Complementarity, Agency Theory, and the God-of-the-Gaps
Naturalism Objections:
“ Why don’t we see miracles today?”
“We can’t know if the miracles happened in the Bible”
“ Given we don’t see men rising from the dead today you can’t expect me to believe a man rose from the dead 2,000 years ago”
Resources:
Why Naturalism Lacks Explanatory Power
What is Scientific Naturalism? J.P. Moreland
God, Naturalism, and the Foundations of Morality: Dr. Paul Copan
Dallas Willard: Knowledge and Naturalism
J.P. Moreland: Naturalism and Libertarian Agency
J.P. Moreland: Scientific Naturalism and the Unfalsifiable Myth of Evolution
J.P. Moreland: The Ethical Inadequacy of Naturalism
Why Christianity Did Need a Miracle To Get Started
Miracles: Do Extraordinary Claims Require Extraordinary Evidence?
Can we know anything if Naturalism is true? Or: A plea for creativity with Theistic Arguments
Extraordinary Claims, Extraordinary Evidence, and Belief in God
Naturalism: A World View: An Overview by Russ Bush
16 Reasons Why I Believe In God: (3) The Regularity of the Universe
Is Naturalism a Simpler Explanation Than Theism? by Paul Copan
Miracles, Intelligent Design,and God-of-the-Gaps: Jack Collins
Answering Nine Objections to the Resurrection of Jesus
The Argument From Miracles: Daniel Bonevac
God’s existence:
“ There is no evidence for God”
“I can’t empirically verify the existence of God. Hence, he must not exist”
“I think religion is just psychological phenomena. It is just a function of the brain”
“ There is no proof for the existence of God”
“ I just don’t think we can know if God exists”
” I think there is maybe a force of some kind. He is in everything”
“ I don’t see what difference it would make if God exists. After all, I am a good person”
“If your belief in God provides you comfort and makes you a better moral person that is fine. But it does not mean it is true.”
“If God exists or created the universe, what caused God”
“ I don’t need God to be a moral person”
Resources:
The Return of the God Hypothesis: Stephen C. Meyer
Is Religious Belief Just a Brain Function?
The Argument from Maths in Seven Quick Points
“God—The Best Explanation”: Paul Copan
The Realm of Doubt: Why Both Skeptics and Theists Have To Exercise Faith
5 Things That Impact Discussions About The Existence of God
Two Sources of the Knowledge of God by Prof. Robert C. Koons (University of Texas at Austin)
The Apologetic Argument: David Snoke
Breaking down the Moral Argument by Glenn Peoples
An Overview of the Moral Argument for God’s Existence by Paul Copan
God, Naturalism, and the Foundations of Morality (PDF download) by Paul Copan
Four lectures on the moral argument by William Lane Craig
Moral Objections to Christianity by David Horner
Did Morals Evolve? by Greg Koukl
Can Moral Objectivism do without God? by Peter Williams
Introduction: Blackwell’s Companion To Natural Theology: J.P. Moreland and William Lane Craig
4 Reasons Why Situational Ethics Doesn’t Work In The Case of Abortion →
If God Made the Universe, Who Made God? By Paul Copan
The Plight of the New Atheism: Gary Habermas
If You Cannot Scientifically Prove Your Belief, Is It Meaningless? By Paul Copan
THINKAPOLOGETICS.COM 
Over at my blog I have a commentor who says that the universe is not past eternal, but that it did not begin to exist. This is a new argument to me.
For context if you’re interested, you can see the comments on this article: http://faithatcrossroads.wordpress.com/2014/08/11/why-i-am-a-christian-part-two-because-there-is-stuff/
Feel free to weigh in if you have anything to add!