Speculah:Kyubey is Madoka's Familiar Theory
This is sort of at odds with the "Kyubey is Evil" theory, being that we don't see Madoka as actually evil. However, it's a subtle bit of iconography that comes to mind when we take a look at what we imagine her symbol will be when/if she ever makes a contract: the teardrop shape that we see on her back during the "Next episode" preview of Ep6, as well as the image for her Soul Gem in the character design. The only character in the series that possesses this bit of iconography is Kyubey, having the great big red teardrop on his back.
If this seems to be a bit too obvious, consider this as well : all the school uniforms have the little teardrop shape between the shoulders where the uniform is buttoned at the top, as shown below. All of the Magical Girls save Kyoko possess this school uniform, with its associated teardrop on the back, marking them as belonging to Madoka in the first place, whether by nakama or other bonds.
Assuming that Madoka herself isn't merely a shell repressing an eldritch horror in the first place (which, admittedly, may be the case), then as her familiar Kyubey is ultimately subservient to the purpose that Madoka wishes for: that people are protected from the depradations of the witches. While he may be quite creepy, he's less deliberately evil and more approaching this from an utterly logical standpoint. For example, during Charlotte's "Dinner", Kyubey's first reaction was to tell the girls to hurry up and make a contract with him. While it may seem opportunistic, in the situation at hand, the most logical point (assuming he was unaware that Homura was present) would be to make a magical girl instantly otherwise Madoka and Sayaka would have died.
As is obvious, his goal is to make a contract with Madoka, but this may ultimately be because he's already aware of what kind of a badass magical girl she is, and, still driven by an admittedly inhuman drive for the protection of humanity and the eradication of witches, seeks her out because he's only doing his job in the most relentlessly logical fashion.
After all, just because Kyubey isn't evil doesn't make him nice.
Alternatively, if Kyubey is a generator of Mahou Shoujo, it may be that Madoka is the "Witch" whose Labyrinth is the world, to whom all Mahou Shoujo are familiars.