Since I happen to be an atheist myself, I am often saddened by the amount of misrepresentations and bad arguments that other atheists use to fight against religion. I will list and debunk some of the more popular ones below.
1. Claiming the Bible is a complete work of fiction
Response: The Bible (OT) should be treated as any ancient history and is not a work, but a collection of works written by people who never thought their works would be collected with those of others. Some are probably totally fictional (Genesis), others, like Judges and Samuel, contain grains of truth (the importance of Shiloh, the existence of David, ect.), and others, like 2 Kings, are history interspersed with fictional accounts. It also contains vital history we as historians would be screwed without, such as the stories of David and Solomon’s temple building, and almost the entire pre-Assyrian 8th century.
2. Claiming Jesus was based on pagan myths
Refutation: See here and J.P. Holding’s “Shattering the Christ Myth”.
3. Claiming “Yam Suph” must be confined to some marshy lake in the NE Delta
Refutation: See AJaL, Section 6.
4. Claiming that, since Exodus (or Israel being in Egypt) is not supported by the Egyptian monuments or papyri, it must have never happened!
Refutation: The only papyri we have recovered from Pi-Ramesse are five wine jar dockets and, if any Exodus did happen, no king of Egypt would mention it on the monuments. Using this argument should be criminalized. Much better arguments include the arguments from Philistines, iron, and Tanis (especially the latter two).
5. Claiming Kadesh is Qudeirat and Ezion Geber is Tell el-Kheleifeh.
Both equations are false. Tell el-Kheleifeh (29°32’50″N, 34°58’50″E) could have been used for small boats, but not for large ships. is possibly Biblical Eloth (the archeology fits). Qudeirat is very likely to be Hazar-Addar, since I can see no other site for it. It may have a hope of a chance of being Kadesh-in-Zin/Waters of Meribah-Kadesh, but this leaves little room for Hazar-Addar or Karka, and Kadesh-in-Zin was outside the promised land.
6. Claiming the Bible is “Bronze Age”