A continuation of the original thread.
NB: This thread is not for discussion of theories; it is only here to list them.
The list below has now been updated by Mladen for this iteration of the thread.
Welcome to the second edition of Compendium of Theories thread. The thread was opened in January 2013, and since then, it became must-read for all those who want to learn about popular and widely-accepted theories on this board. Since last January, the thread was updated several times, and this opportunity demands the updated list of everything that has been theorized in the past year.
Please have in mind that this thread serves as the encyclopedic list of the theories, analyses and threads on this board. The whole point of this thread is to have organized list of many great and outside-the-box ideas that were posted at some point on this board. This thread is not for discussing the theories, or questioning them in any way, as it is your guide through the thousands and thousands of threads and posts on General section of this forum. We also warmly invite you to link us all the theories that you feel deserve to be included, as also to give us feedback of what we might have missed.
This time, we will update the Compendium with the links from the Citadel that might give you the better understanding of certain theories. Also, we will divide the list into several categories that will make your search easier.
Spoiler tags added for length: