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
Philo
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