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These are secular magazines which are available online and/or in print. All are off site.

American Atheist Magazine
A Journal of Atheist News and Thought

Free Inquiry
Magazine of the Council for Secular Humanism

The Freethinker
A British Secular Humanist Journal

Freethought Today
The Only Freethought Newspaper in North America

The Humanist
A Magazine of Critical Inquiry and Social Concern

The Journal of the Society of Humanist Philosophers

The Secular Humanist Bulletin
The Associate Members’ Newsletter of the Council for Secular Humanism

Secular Nation
A Voice for Atheists and a Standard Bearer for Atheism

The Skeptical Inquirer
The Magazine for Science and Reason

Skeptic Magazine
A quarterly journal promoting science and critical thinking.

The Skeptic
A Skeptical Look at Pseudoscience and Claims of the Paranormal in the U.K.

Truth Seeker
The World’s Oldest Freethought Publication; published since 1873