God is Dead, we have Thrown Twigs at him.

As far as I can tell, the most popular argument among atheists when confronted with the fact that their worldview can't explain the existence of the universe, objective morality, self-consciousness, life, logic, or ascetics, is that they can't believe in the Christian God because he's done so many evil things.  Besides the fact that atheists don't have any reason or basis for holding God to any kind of morality, I will try to argue that God is good.

Of course, the thing that really makes this a fools errand is that to the atheist, what is good is what makes him feel good and what is bad is what makes him feel bad.  Because of this, it is impossible to argue that what someone does is good because his interpretation of good is that which he believes is good.  Of course, this leaves him in the rather uncomfortable position of not being able to say that what anyone does is bad, meaning he can't say that it would be evil for me to shoot him in the head.  Because of this, I believe that the only way to answer this argument is from the perspective of Christian values, since an atheist can at least point out if God and therefore Christianity is inconsistent.  (Even though atheists still can't give objective basis for using the law of non-contradiction, I feel an obligation to use it in my defense, as the Christian worldview does support the law of non-contradiction.)  

Lets look at some specifics.  II Kings 2:23-25:

"He went up from there to Bethel, and while he was going up on the way, some small boys came out of the city and jeered at him, saying, "Go up, you baldhead! Go up, you baldhead!" And he turned around, and when he saw them,he cursed them in the name of the LORD. And two she-bears came out of the woods and tore forty-two of the boys.From there he went on to Mount Carmel, and from there he returned to Samaria."

In this passage, we see God maim and possibly kill 42 boys.  Terrible, right?  Well, we'll see.  One thing that atheists have trouble understanding about Christian Theology is that Christians believe that sin is a serious matter.  Although Christ preached that we as Christians should forgive as God forgave us, God is not held to that standard.  God is holy, and it is part of his very nature to punish sinners for their sins.  In this case, we see Children who are not only treating an elder with disrespect, (thus breaking both the 5th and 6th commandments)  they are also doing so to a prophet, God's servant and mouth to communicate to his people, the Israelites, thus also breaking the 3rd commandment by disrespecting God's representative.  If someone mistreated the President, the US would take it as an offense.  Such an act would be an act of disrespect against the US and would belittle and degrade the name of the US (not that I think that that's a sin, it's just an example).  As question 100 of the Heidelberg Catechism attests to, this is a serious offense:

Is then the profaning of God's name, by swearing and cursing, so heinous a sin, that his wrath is kindled against those who do not endeavour, as much as in them lies, to prevent and forbid such cursing and swearing? 

It undoubtedly is, for there is no sin greater or more provoking to God, than the profaning of his name; and therefore he has commanded this sin to be punished with death.

Because this sin is so heinous in God's eyes, being killed or maimed for committing it (not to mention the other two comandments, which God also commanded to be punished by death) is perfectly just and righteous.  Some may say that that doesn't seem fair to them, but since it obviously seems fair to God, they have no grounds to accuse him for doing wrong.  They may also say that they wouldn't want to believe in a God like that, but they must remember that whether they want God to exist or not has nothing to do with whether he actually exists or not.  It only has to do with whether they're right or wrong in their subjective impressions.

But what about evil in general?  Why does God allow evil in the first place that requires punishment?  After all, you said that this God was omnipotent and omnibenevolent, right?  How could such a God allow the evil and the death that we see all around us?  This is admittedly a difficult question two answer, however, I do not believe that it is necessarily a crushing blow to the Christian.  After all, when you think about it, for God to stop evil he would have had to create a bunch of robots with no free will.  One can understand why God would want something more than little humanoid robots, since being loved by something with no free will is hardly any love at all.  But couldn't God have created a world in which free will existed but sin was still impossible?  Umm. . . no.  If sin is impossible, then free will has already been restricted.  But isn't God cruel to create a world that he knew would result in astronomical pain and suffering?  Well, I suppose you might think so, but God is no more responsible for the evil in the world than any person is for the sins of their children, seeing as they brought them into existence.  Furthermore, as terrible as the pain and suffering in this would is, the joy and fulfillment that can come from a life lived for Christ can certainly surpass it.  Thus, God refrains from preventing evil because he loves us and wants to maintain a real relationship with us, rather than controlling us like robots.

Obviously there are many other variations on these basic ideas, but I believe that most of them can be refuted with the same or similar arguments.  Remember, even if an atheist still thinks that what God has done is evil, he has no basis for what is evil.  He can only claim that God has contradicted himself and therefore that God cannot form a solid basis for morality.  Of course, this claim also is untrue, since, as we have seen, the actions some perceive as evil are best explained by God's consistency.