Books, articles, documentaries, etc..
For secondary sources, the books that I believe are the best in regards to al Qaeda's origins are:
Alex Strick van Linschoten and Felix Kuehn, An Enemy We Created: The Myth of the Taliban-Al Qaeda Merger
Fawaz Gerges, The Far Enemy: Why Jihad Went Global
Lawrence Wright, The Looming Tower: Al Qaeda and the Road to 9/11
Steve Coll, Ghost Wars
Thomas Hegghammer, Jihad and Saudi Arabia: Violence and Pan-Islamism since 1979
Not sure how far back you want to go, but here's a few:
The Manchester Manual was discovered in an Al Qaeda safehouse in Manchester, England in 2000. It details Al Qaeda's philosophy, justification for attacks, and operating methods for blending into Western society, and how to actually carry out covert terrorist attacks.
Wikipedia: https://en.wikipedia.org/wiki/Al_Qaeda_Handbook
Actual PDF of Manual (Translated to English: http://www.justice.gov/sites/default/files/ag/legacy/2002/10/08/manualpart1_1.pdf
The Letters from Abottabad are letters from/to Osama bin Laden and other high ranking members of the core Al Qaeda group. They were recovered by US Navy Seals during the raid in 2010 that killed Osama Bin Laden. The letters are from around 2005-2010 from the time Osama lived in Abottabad. They offer a fascinating insight into high ranking Al Qaeda's assessment of how the conflict with the West was going, featuring Osama chiding his subordinates for failing to carry out spectacular attacks reminiscent of 9/11, or chiding then-leader of AQI (now better known as ISIS) Abu Musab al Zarqawi about alienating the Umma (world community of Muslims) with his extraordinarily bloody campaign of bombings on civilians in Iraq around 2006-2007.
Original Letters / Translated Letters: https://www.ctc.usma.edu/posts/letters-from-abbottabad-bin-ladin-sidelined
Osama bin Laden's Declaration of Jihad Against the Americans Occupying the Land of the Two Holiest Sites, this document is Osama's public justification for killing American & allied civilians / military wherever they can be found. Interestingly, being a devote Sunni muslim, Osama believed it a religious obligation to "warn" his enemies that a state of war now existed between them & his group. This declaration was originally written in 1996, about two years before Al Qaeda became a household name for carrying out the dual bombings of the US Embassies in Tanzania and Kenya.
English Translation: https://en.wikisource.org/wiki/Osama_bin_Laden%27s_Declaration_of_War
Guarding Bin Laden is a firsthand account of one of Osama bin Laden's personal bodyguards from the late 80s during the Soviet-Afghan war to a few months after the attacks of 9/11. Written by a guy named Nasser al-Bahri but whose kunya was Abu Jandal ("father of death"), who has now renounced violent jihad but still believes in the core tents of Al Qaeda and extremist apocalyptic Islam, who is living openly in Yemen.
The most interesting thing about this book is that it offers a keen insight into Osama's mindset, and also his daily activities (including being everyone's favorite player on their team whenever Al Qaeda played volleyball, because he was so tall). Osama, evidently, was against the use of nuclear weapons, where as his lieutenant (and present leader of Al Qaeda, Ayman al-Zawahiri, was very much so in favor of their use).
Also interesting of note, it's fascinating to compare the account of Al-Bahri and FBI agent / investigator / interrogator Ali Soufan (author of an amazing Al Qaeda book called The Black Banners). Al-Bahri was interrogated by Soufan, and it's strange to read two wildly different accounts of the same interrogations by two wildly different people. That book, by the way, is a great read in general on Al Qaeda and especially as a companion to this book.
Ebook: Nasser al-Bahri. “Guarding bin Laden: My Life in Al-Qaeda.” iBooks. https://itun.es/us/xnpSM.l
Ebook: Ali H. Soufan & Daniel Freedman. “The Black Banners: The Inside Story of 9/11 and the War Against al-Qaeda.” iBooks. https://itun.es/us/5PhCB.l
I could probably go on, but I need to get to work. If there's any more interest I can compile more original documents or just a general list of great books on Al Qaeda. I have a whole section of my iBooks dedicated to Al Qaeda, haha. Let me know if you got any comments or questions I could help out with.
Inside the Jihad by Omar Naisiri is a favorite of mine, about a GIA member who defects to French intelligence and attends some Al Qaeda camps for the intel community's benefit. There are also first hand Chechnyan stories in English about their war with Russia, which helps to understand the Al Qaeda background.