http://www.arsdisputandi.org/publish/articles/000163/article.pdf

The preceding is an argument between an atheist and a christian, and contains many Atheistic arguments, as well as their christian counter-points.

http://muse.jhu.edu/journals/journal_of_the_history_of_ideas/v063/63.2goodrum.html

This link contains a look at the atheistic and atomistic views on spontaneous generation of human beings.

http://www.infidels.org/library/modern/mathew/arguments.html

This link is a library which documents quite a few well known atheist viewpoints, as well as counterpoints found by the theistic public in order to disprove them.

http://atheism.about.com/od/argumentsagainstgod/Arguments_Against_God_Atheological_Arguments_for_Atheism.htm

This link is another library for atheistic arguments that can easily be accessed.

http://www.arsdisputandi.org/publish/articles/000377/article.pdf

This link contains a PDF which looks at a few atheists who are part of the New Atheist Movement, their arguments, and theistic counterpoints.