It seems that one of the prevailing arguments against the goodness of the God of the Bible is the actions of God cited in that very book. To use these actions as evidence against God's nature, one is accepting the testimony of Scripture as a valid source in supporting this argument. Presumably if the Christian God exists then the Bible tells about whom this God is, and as such the testimony of this book is used to invalidate the claim of God's goodness.
In all fairness, one should look at the whole testimony concerning the nature of this God and consider the following.
King David, after sinning against God, was faced with the choice of being punished by the hands of his enemies or by God himself. To which David responded, "let us fall into the hands of the Lord, for His mercy is great; but do not let me fall into the hands of men" (2 Samuel 24:14). David, a contemporary of the Old Testament, fully knowledgeable about the events of his day and the actions of God said wholeheartedly that he would rather face God's judgment than man's. He believed God to be more merciful than man.
Moses who saw God's actions time and again cried out to God, "If your Presence does not go with us, do not send us up from here" (Exodus 33:15). He did not want to lead the people anywhere without the Presence of God going with them.
Both David and Moses are contemporaries of the days when God unleashed judgment in the earth by way of calamity or war, and yet both saw the Lord's mercy is great and that His Presence is greatly desirable.
These are only two of the many examples of the men and women who trusted in the Lord and spoke of His goodness and mercy. While Christians often do an injustice by depicting God as a Being who is tolerant of sin and who would never exact judgment upon people due to their sin, it is just as inaccurate for atheists to champion God as a vindictive genocidal maniac. If we are looking at the same Bible we ought to be able to see a God who is holy, good, and just.
C.S. Lewis gives the imagery in The Chronicles of Narnia of a good, but not a tame Lion. God is good and merciful while at the same good and just. The Bible says that the wages of sin is death. It also says that Jesus came to give life to those trapped in this sin; to provide mercy and righteousness to the sinner by offering to become united with us thereby making us clean as He is clean. Jesus took on the wages of sin for us. What greater mercy and love can there be?