Forgive me for not reading the entire thread, but I agree entirely with C.A. What is the basis for atheist's morality? Is it simply a Machiavellian motivation? (I won't kill you and take all your things, because it serves my purpose at this time.) Or, is there a deeper reason for being moral?
http://en.wikipedia.org/wiki/Euthyphro_dilemma
So... What is the basis for atheistic morality? How do you know what is "good"?
To summarize Euthyphro: How do theists know what is good? All they have is a book written by other people who presume to speak for God. But then they are confronted by the following two problems:
1. Is the good determined by God, or does God recognize what is good?
2. Why should we trust the writers of sacred texts to be speaking for God, and why doesn't God simply speak for himself?
To answer the first: If the former, then the good is arbirtary. If the latter, then the good is objective and it doesn't matter if we believe in God or not.
To answer the second: Anybody can write down something and claim that it comes from God, but if they are wrong then it should be discarded, and if they are right then you must refer to the first objection.
To answer your main question: How do atheists know what is good? Many different ways. There is no single atheistic moral standard, because all atheism means is not believing in gods. So available to atheists are every moral standard which are not theistic, which are many. To mention a few:
Ethical egoism
Hedonism
Existentialism
Utilitarianism
Natural realism
Objectivism
Moral relativisim
Cultural relativism
etc.
Some models are consequentialist (emphasize the consequences of an act) whereas others are more deontological (derived from rules). If you believe that ethics stem from empathy and emotions, you're more likely to be a Humean, whereas if you believe that ethical rules should be derived from an imperative which all people should be able to follow in every situation, you're more likely to be a Kantian. If you believe that the good of the many is to be sought then you're a utilitarian (John Stuart Mill) whereas if you believe that the ultimate moral society could be derived from behind a veil of ignorance from which every individual should be able to determine the rules without knowing what their role in society would turn out to be, then you're a Rawlsian (John Rawls). If you're a cultural relativist, then you believe that the good is entirely determined by culture and cannot be judged by outsiders. If you're an individual moral relativist, then you believe that the good is entirely determined by individuals. If you're a hedonist, then you believe that the good is determined by what is pleasurable.
In essence, you're asking me to summarize the entirety of moral philosophy. That's not something I care to do-- all I can really do is tell you to check out a book on the subject and find out for yourself. It's not something that can be fully discussed on an internet forum, but I've tried to give you an idea of the scope of possibilities.