A good scriptural apologetics site I found recently is www.christian-thinktank.com, which provides explanations for difficult biblical passages and issues. I can't vouch for everything yet, but one article I liked gives a good explanation for the ordered attacks and killings of Canaanites and Amalekites in the Old Testament, and similar OT controversies.
In John’s Gospel we have an emphasis on Jesus that is unique compared to the other gospels. John not only emphasizes his deity, but his mysteriousness. The reader is left with an impression of Jesus as a mystical teacher, in the sense that his words and actions are not only those of a profound religious teacher, but of one who is other-worldly. So often in this gospel we read of Jesus making statements that the crowds, the religious teachers, and even his own disciples sometimes could not fathom. For starters, there are the “I am” statements (e.g., I am the bread of life; I am the living water; I am the good shepherd; I am the way, the truth, and the life), which were clearly claims to divinity, for these statements in the Jewish context referred to God’s title “I am,” given when Moses inquired of his name at the burning bush. Jesus makes much use of mystical metaphors like these and others, like all the ‘day’ and ‘night’ references in this book, which portrays him as mystical or my