Here's a whole slew of resources for the study of esotericism and secret societies that I have gathered, originally placed on ATS where the content is generally ignored now.
Societies with secrets and clandestine organizations:
Online resources:
Pietre-Stones Review of Freemasonry
Freemason Information
Canonbury Masonic Research Centre
Freemasonry Today
The Centre for Research into Freemasonry and Fraternalism - University of Sheffield (The centre is presently shut, though the website remains)
ASRFF News - official blog of ASRFF - The Academic Society for Research into Freemasonry and Fraternalism
Masonic Info
Masonic Dictionary
Phoenixmasonry, Inc.
Phoenixmasonry, Inc. - Extensive list of ebooks on Masonry
Bavarian Illuminati - Home of the Original Writings of the Bavarian Illuminati
Illuminati Conspiracy Part One: A Precise Exegesis on the Available Evidence
(Bavarian Illuminati)
Illuminati Conspiracy Part Two: Sniffing out Jesuits
(Bavarian Illuminati)
Illuminati of Bavaria
Timeline of the Authentic Tradition
Antiquities of the Illuminati
US Grand Lodge - Ordo Templi Orientis
Theodor Reuss' Ordo Templi Orientis rituals
Thelemapedia
The Ancient Mystical Order Rosae Crucis
International Institute of Social History - Secret societies: A very short history
Wikipedia list of secret societies, attendant material and mythologies
Holy Terror: The Rise of the Order of the Assassins
Mysticism, Germanentum, and the Thule-Gesellschaft by Devorah McGinnis
Podcasts:
Masonic Central Podcast - Philosophy
Masonic Central Podcast - Spirituality
PDF books:
The Rosicrucian Enlightement - Frances A. Yates
The Origins of Freemasonry - Scotland's Century 1590 to 1710 - by David Stevenson
The Secret History of Freemasonry: Its Origins and Connection to the Knights Templar by Paul Naudon
Born in Blood: The Lost Secrets of Freemasonry by John J. Robinson
The Arcane Schools: A Review Of Their Origin And Antiquity With A General History Of Freemasonry by John Yarker
Morals And Dogma By Albert Pike
The secret societies of all ages and countries : a comprehensive account of upwards of one hundred and sixty secret organizations, religious, political, and social, from the most remote ages down to the present time ... and other mysterious sects - Vol. I by Charles William Heckethorn
The secret societies of all ages and countries : a comprehensive account of upwards of one hundred and sixty secret organizations, religious, political, and social, from the most remote ages down to the present time ... and other mysterious sects - Vol. II by Charles William Heckethorn
History of Freemasonry Throughout the World - R.F. Gould
An Encyclopedia of Freemasonry by Albert G. Mackey
Stellar Theology and Masonic Astronomy - Robert Hewitt Brown
4shared - 500 Masonic ebooks
Two PDF books on the Order of the Assassins:
The Order of Assassins - Marshall G.S. Hodgson
The History of the Assassins - Joseph von Hammer
Tragedy & Hope: A History of the World in Our Time by Carroll Quigley.
The Anglo-American Establishment - by Carroll Quigley
America's Secret Establishment: An Introduction to the Order of Skull and Bones by Antony C. Sutton
Offline resources:
Living the Enlightenment: Freemasonry and Politics in Eighteenth-Century Europe by Margaret C. Jacob
Fire in the Minds of Men: Origins of the Revolutionary Faith by James H. Billington
Perfectibilists: The 18th Century Bavarian Order of the Illuminati by Terry Melanson
Qadosh: The Johannite Tradition by Jonathan Sellers
Western esoterica/occult philosophy:
Online:
Amsterdam Hermetica - Western Esotericism in the Academy
European Society for the Study of Western Esotercism
Links to full length articles from Esoterica: The Journal of Esoteric Studies:
Esoterica Journal
Gnostic Info
Gyllene Gryningen Blogspot
The Craftsman's Trowel Blogspot
Internet Sacred Text Archive
The Library of Hermetic Philosphy in Amsterdam
Twilight Grotto - Esoteric Archives
The Warburg Institute Library
The Hermetic Library
The Alchemy Website
Society for the History of Alchemy and Chemistry
The Rosicrucian Library
Theosophy Library Online
The Occult (Bit torrent resource site for esoterica)
Thelemapedia
Salamander and Sons - Esoteric, occult and arcane book publishers
Rubaphilos.com
Transalchemy.com's Picasa page featuring a plethora of alchemical imagery and art:
key.universe's Picasa page: Alchemy
ifdawn.com | The Tree of Life (The Original, since 1994)
BBC - h2g2 - The Secret Art of Alchemy
Much information on John Dee available in this post.
Fortean Times: The Occult World of CG Jung
- How a near-death experience transformed the psychologist's attitude to the world of mysticism and magic
PDF books:
A History of Magic and Experimental Science Vol. I - Lynn Thorndike
A History of Magic and Experimental Science Vol. II - Lynn Thorndike
Dictionary of Gnosis and Western Esotericism edited by Wouter J. Hanegraaff
The Occult Underground - James Webb
Against the Modern World: Traditionalism and the Secret Intellectual History of the Twentieth Century by Mark Sedgwick
The Occult Roots of Nazism: Secret Aryan Cults and Their Influence on Nazi Ideology by Nicholas Goodrick-Clarke
Black Sun: Aryan Cults, Esoteric Nazism, and the Politics of Identity by Nicholas Goodrick-Clarke
Hitler's Priestess: Savitiri Devi, the Hindu-Aryan Myth, and neo-Nazism by Nicholas Goodrick-Clarke
The lightning and the sun
by Savitri Devi
The Esoteric Origins of the American Renaissance by Arthur Versluis
The Red Book by Carl Jung
The Medieval Manichee: A Study of the Christian Dualist heresy - by Steven Runciman
The Refiner's Fire: The Making of Mormon Cosmology, 1644-1844 by John L. Brooke
The Occult Philosophy of the Elizabethan Age by Frances A. Yates
The Art of Memory by Frances A. Yates
Giordano Burno and the Hermetic Tradition by Frances A. Yates
John Dee: Interdisciplinary Studies in English Renaissance Thought (International Archives of the History of Ideas) by Stephen Clucas (Editor)
Three Books on Life (Medieval and Renaissance Texts and Studies) by Marsilio Ficino, Carol V. Kaske, John R. Clark
Eternal Hermes: From Greek God to Alchemical Magus by Antoine Faivre
Occult America: The Secret History of How Mysticism Shaped Our Nation by Mitch Horowitz
Rar'd html files:
Gnosis and Hermeticism from Antiquity to Modern Times (S U N Y Series in Western Esoteric Traditions) by R. van den Broek, Wouter J. Hanegraaff
Access to Western Esotericism (Suny Series in Western Esoteric Traditions) by Antoine Faivre
Podcasts:
Occult of Personality Podcast
Gnostic Media Podcast
Alchemically Braindamaged Podcast
Some excellent podcasts here from Melvyn Bragg's "In Our Time" on the subject of Esoterica:
Renaissance Magic
Renaissance Astrology
The Music of the Spheres
Rudolph II
Catharism
Carl Gustav Jung
Pythagoras
Zoroastrianism
Offline resources:
The Occult Establishment - James Webb
The Western Esoteric Tradition: A Historical Introduction by Nicholas Goodrick-Clarke
John Dee's Conversations with Angels: Cabala, Alchemy, and the End of Nature by Deborah E. Harkness
John Dee's Natural Philosophy: Between Science and Religion by Nicholas Clulee
John Dee's Occultism: Magical Exaltation Through Powerful Signs (Suny Series in Western Esoteric Traditions) by Gyorgy E. Szonyi
Hegel and the Hermetic Tradition by Glenn Alexander Magee