[edit: I've included sources from 911: Ultimate Truth, as well as your suggestions, Ardvan]
While reading Secret History, I kept a list of cited sources that I felt were most important. As the bibliography is quite daunting. Please feel free to add to the list, or let me know if a certain source isn't really that stellar. I've included a small list at the end of books I've come across (I haven't read them all) that seem to relate to some of the ideas presented in SH, as well. [edit: these are now in the main sections, but in []'s]
Esoterica
Chittick, William - The Sufi Path of Knowledge
Fulcanelli - The Mystery of the Cathedrals
Fulcanelli - The Dwellings of the Philosophers
Gurdjieff, G.I. - Beelzebub's Tales to His Grandson
Mouravieff, Boris - Gnosis I, II, & III
Ouspensky, P.D. - In Search of the Miraculous
Ovason, David - Zelator
Psychopathy and Ponerology
Cleckley, Hervey - The Mask of Sanity
Hare, Robert - Without Conscience
Lobaczewski, Andrew - Political Ponerology
Scott, Ernest - The People of the Secret
Simon, George - In Sheep's Clothing
Stout, Martha - The Sociopath Next Door
[Gatto, John Taylor - Dumbing Us Down]
9/11
Griffin, David Ray - The New Pearl Harbour
Griffin, David Ray - The 9/11 Commission Report: Omissions and Distortions
Meyssan, Thierry - Pentagate
Meyssan, Thierry - 9/11 The Big Lie
Ostrovsky, Victor - By Way of Deception
[Raimondo, Justin - The Terror Enigma]
Castaneda
Castaneda, Carlos - The Teachings of Don Juan
Castaneda, Carlos - A Separate Reality
Castaneda, Carlos - Journey to Ixtlan
Castaneda, Carlos - Tales of Power
Castaneda, Carlos - The Second Ring of Power
Castaneda, Carlos - The Eagle's Gift
Castaneda, Carlos - The Fire from Within
Castaneda, Carlos - The Power of Silence
Castaneda, Carlos - The Art of Dreaming
Castaneda, Carlos - The Active Side of Infinity
[Taisha Abelar - The Sorcerer's Crossing: A Woman's Journey]
[Florinda Donner-Grau - Being-In-Dreaming]
Grail Mythology and Shamanism
Blake and Lloyd - The Keys to Avalon
Campbell, Joseph - Hero with a Thousand Faces
Eliade, Mircea - Shamanism
Littleton and Malcor - From Scythia to Camelot
O'Shea, Stephen - The Perfect Heresy
Weston, Jessie - The Legend of Sir Perceval
Weston, Jessie - From Ritual to Romance
Geomythology, Catastrophism, and the Scientific Thought Police
Baillie, Michael - From Exodus to Arthur
Bakker, Robert - The Dinosaur Heresies
Cremo, Michael - Forbidden Archaeology
Flem-Ath, Rand - When the Sky Fell
Fomenko, Anatoly - History: Fiction or Science?
Hapgood, Charles - Maps of the Ancient Sea Kings
Lethbridge, T.C. - The Power of the Pendulum
Muck, Otto - Secret of Atlantis
Santillana and Von Dechend - Hamlet's Mill
Shreeve, James - The Neandertal Enigma
Velikovsky, Immanuel - Worlds in Collision
[Collins, Andrew - Gods of Eden] [sound technology on pyramids]
[Cruttenden, Walter - Lost Star of Myth and Time] [second Sun hypothesis]
[Henry, Roger - Synchronized Chronology] [summary of Velikovsky's Ages in Chaos series]
[Tedlock, Barbara - The Woman in a Shaman's Body] [I've read good things about this one]
[Wilson, Colin - From Atlantis to the Sphinx] [apparently covers a lot of the same ground, although he's ill-informed on Fulcanelli, among other things]
Egypt, Israel, and Who Wrote the Bible
Collins, Andrew - Tutankhamen: The Exodus Conspiracy
Finkelstein, Israel - The Bible Unearthed
Fox, Hugh - Gods of the Cataclysm
Friedman, Richard - Who Wrote the Bible
Gershom, Yonassan - Beyond the Ashes
Gorenberg, Gershom - The End of Days
Halsell, Grace - Forcing God's Hands
Joseph, Frank - The Lost Pyramids of Rock Lake
Koestler, Arthur - The Thirteenth Tribe
MacDonald, Kevin - The Culture of Critique
Redford, Donald - Egypt, Canaan, and Israel in Ancient Times
Wunderlich, Hans George - The Secret of Crete
[Dever, William - Who Were the Early Israelites?]
UFOs and the National Security State
Bramley, William - The Gods of Eden
Dolan, Richard - UFO's and the National Security State
Jessup, Morris - The Case for the UFO
Marrs, Jim - Alien Agenda
Vallee, Jacques - Passport to Magonia
Vallee, Jacques - Messengers of Deception
[Druffel, Ann - Firestorm: Dr. James E. MacDonald's Fight for UFO Science]
While reading Secret History, I kept a list of cited sources that I felt were most important. As the bibliography is quite daunting. Please feel free to add to the list, or let me know if a certain source isn't really that stellar. I've included a small list at the end of books I've come across (I haven't read them all) that seem to relate to some of the ideas presented in SH, as well. [edit: these are now in the main sections, but in []'s]
Esoterica
Chittick, William - The Sufi Path of Knowledge
Fulcanelli - The Mystery of the Cathedrals
Fulcanelli - The Dwellings of the Philosophers
Gurdjieff, G.I. - Beelzebub's Tales to His Grandson
Mouravieff, Boris - Gnosis I, II, & III
Ouspensky, P.D. - In Search of the Miraculous
Ovason, David - Zelator
Psychopathy and Ponerology
Cleckley, Hervey - The Mask of Sanity
Hare, Robert - Without Conscience
Lobaczewski, Andrew - Political Ponerology
Scott, Ernest - The People of the Secret
Simon, George - In Sheep's Clothing
Stout, Martha - The Sociopath Next Door
[Gatto, John Taylor - Dumbing Us Down]
9/11
Griffin, David Ray - The New Pearl Harbour
Griffin, David Ray - The 9/11 Commission Report: Omissions and Distortions
Meyssan, Thierry - Pentagate
Meyssan, Thierry - 9/11 The Big Lie
Ostrovsky, Victor - By Way of Deception
[Raimondo, Justin - The Terror Enigma]
Castaneda
Castaneda, Carlos - The Teachings of Don Juan
Castaneda, Carlos - A Separate Reality
Castaneda, Carlos - Journey to Ixtlan
Castaneda, Carlos - Tales of Power
Castaneda, Carlos - The Second Ring of Power
Castaneda, Carlos - The Eagle's Gift
Castaneda, Carlos - The Fire from Within
Castaneda, Carlos - The Power of Silence
Castaneda, Carlos - The Art of Dreaming
Castaneda, Carlos - The Active Side of Infinity
[Taisha Abelar - The Sorcerer's Crossing: A Woman's Journey]
[Florinda Donner-Grau - Being-In-Dreaming]
Grail Mythology and Shamanism
Blake and Lloyd - The Keys to Avalon
Campbell, Joseph - Hero with a Thousand Faces
Eliade, Mircea - Shamanism
Littleton and Malcor - From Scythia to Camelot
O'Shea, Stephen - The Perfect Heresy
Weston, Jessie - The Legend of Sir Perceval
Weston, Jessie - From Ritual to Romance
Geomythology, Catastrophism, and the Scientific Thought Police
Baillie, Michael - From Exodus to Arthur
Bakker, Robert - The Dinosaur Heresies
Cremo, Michael - Forbidden Archaeology
Flem-Ath, Rand - When the Sky Fell
Fomenko, Anatoly - History: Fiction or Science?
Hapgood, Charles - Maps of the Ancient Sea Kings
Lethbridge, T.C. - The Power of the Pendulum
Muck, Otto - Secret of Atlantis
Santillana and Von Dechend - Hamlet's Mill
Shreeve, James - The Neandertal Enigma
Velikovsky, Immanuel - Worlds in Collision
[Collins, Andrew - Gods of Eden] [sound technology on pyramids]
[Cruttenden, Walter - Lost Star of Myth and Time] [second Sun hypothesis]
[Henry, Roger - Synchronized Chronology] [summary of Velikovsky's Ages in Chaos series]
[Tedlock, Barbara - The Woman in a Shaman's Body] [I've read good things about this one]
[Wilson, Colin - From Atlantis to the Sphinx] [apparently covers a lot of the same ground, although he's ill-informed on Fulcanelli, among other things]
Egypt, Israel, and Who Wrote the Bible
Collins, Andrew - Tutankhamen: The Exodus Conspiracy
Finkelstein, Israel - The Bible Unearthed
Fox, Hugh - Gods of the Cataclysm
Friedman, Richard - Who Wrote the Bible
Gershom, Yonassan - Beyond the Ashes
Gorenberg, Gershom - The End of Days
Halsell, Grace - Forcing God's Hands
Joseph, Frank - The Lost Pyramids of Rock Lake
Koestler, Arthur - The Thirteenth Tribe
MacDonald, Kevin - The Culture of Critique
Redford, Donald - Egypt, Canaan, and Israel in Ancient Times
Wunderlich, Hans George - The Secret of Crete
[Dever, William - Who Were the Early Israelites?]
UFOs and the National Security State
Bramley, William - The Gods of Eden
Dolan, Richard - UFO's and the National Security State
Jessup, Morris - The Case for the UFO
Marrs, Jim - Alien Agenda
Vallee, Jacques - Passport to Magonia
Vallee, Jacques - Messengers of Deception
[Druffel, Ann - Firestorm: Dr. James E. MacDonald's Fight for UFO Science]