Speculah:Witches as Fallen Magical Girls Theory
As of episode 8, one of the origins of witches has been confirmed. Sayaka's soul gem that never was cleansed causes her to transform to a witch.
Episode 2 shows that witches and magical girls both possess some sort of gem, which is called Grief Seed in the former case and Soul Gem in the latter. We also know from Mami's explanations that people can become Magical Girls by exchanging a wish for a Gem, while Witches, on the other hand, originates from a curse. It has also been pinpointed that in a way, a curse is nothing else than a "negative wish", i.e. the wish to harm someone.
But the similarity between both gems owners is greater than that. As seen at the end of episode 2, a Grief Seed looks like a muddied Soul Gem. Furthermore, Mami states that by using magic, her Soul Gem became dirty, and that she can use the Grief Seed to absorb this "mud" and make it clean again, therefore restoring its magical powers. As a side note, we learn in the same scene that a Grief Seed can be used more than once (Mami gives hers to Homura stating that "it can still be used once").
Now, what we can infer from that is that witches may just be "fallen magical girls". Granted that using magic makes your Gem dirty, and the only way to restore them is to kill witches and steal their Seeds, there could be magical girls that used up all their powers without ever recharging them (because they weren't aware of it or because they refused to kill witches), and so became witches themselves. On the other hand, no explanation has been given so far (episode 2) as to whether a witch can clean their seed (and hence turn back into a magical girl if the aforementioned theory is correct), though as of episode 9, this is proven to be highly unlikely if at all possible.
Alternatively, it is possible that a Witch's Labyrinth is in fact the manifestation of a wish. Upon completion of a contract and fulfillment of a magical girl's wish, she is imprisoned within a false world in which her wish appears to be realized. To other humans, however, the "world" in which the magical girl now lives is a Witch's Labyrinth -- a hedonistic dream, generated by the Witch's strongest desire. By this theory, all magical girls who are not killed before completion of a contract are eventually rendered witches. In effect, the propagation of familiars may be thought of as a mechanism to ensure the continuation of a Witch's dream -- by feeding on the hopes and dreams of others. Relatedly, the cleaning/recharging of a Soul Gem may indicate that the wish of a magical girl feeds on the dreams of defeated witches.