These are secular magazines which are available online and/or in print. All are off site.
American Atheist Magazine
Quarterly Magazine of Atheist News and Thought: Online Edition
Magazine of the Council for Secular Humanism
A British Secular Humanist Journal
The Only Freethought Newspaper in North America
A Magazine of Critical Inquiry and Social Concern
The Open Society
The Journal of the New Zealand Association of Rationalists and Humanists
The Journal of the Society of Humanist Philosophers
The Secular Humanist Bulletin
The Associate Members' Newsletter of the Council for Secular Humanism
A Voice for Atheists and a Standard Bearer for Atheism
The Skeptical Inquirer
The Magazine for Science and Reason
A quarterly journal promoting science and critical thinking.
A Skeptical Look at Pseudoscience and Claims of the Paranormal in the U.K.
The Skeptical Review
A Critical Examination of the Bible Inerrancy Doctrine
The Journal of Independent Thought