Magazines:

Calfornia Freemason (US): www.freemason.org/news_events/index.php

Empire State Mason (US): www.esmason.com/news.html

Freemasonry Today (UK) www.freemasonrytoday.com/

Freemason's Press (US): www.freemasonspress.info/

LodgeroomUK Magazine (UK): www.lodgeroomus.net/downloadcenter/index.php?act=category&id=1

Masonic Forum Magazine (Rom): www.masonicforum.ro/

MQ now defunct but old issues here: www.mqmagazine.co.uk/site/index.php

Pennsylvania Freemason (US): www.pagrandlodge.org/freemason/index.html

Rising Point (US): www.bonisteelml.org/MASONIC_REVIEW.htm

Rough Aslar (Can): http://roughashlar.com/

Scottish Rite Journal (US): http://www.srmason-sj.org/council/journal/srj.htm

S. Australian & NT Freemason (AUS): http://www.freemasonrysaust.org.au/magazine.html

The Working Tools Magazine (US): http://hawthornefortitude200.com/jooma/index.php?option=com_frontpage&Itemid=1

Books:

Lodgeroom UK's Ebooks: www.lodgeroomus.net/downloadcenter/index.php?act=category&id=5

Pietre Stone's Review, Index of online books: www.freemasons-freemasonry.com/masonic_books_online.html

Phoenix Museum of Masonry, Ebook Library: www.phoenixmasonry.org/masonicmuseum/tableofcontents.htm

Sacred Texts, Masonic Index: www.sacred-texts.com/mas/index.htm

Morals & Dogma: www.sacred-texts.com/mas/md/index.htm

Papers:

Lodgeroom UK's Research Papers: www.lodgeroomus.net/downloadcenter/index.php?act=category&id=4

Pietre Stone's Papers: www.freemasons-freemasonry.com/scholars.html & www.freemasons-freemasonry.com/abcindex.html 

Gary Dryfoos's Papers Page (US): http://web.mit.edu/dryfoo/www/Masonry/Essays/

You can't read the Square online, you can only order it to buy.