Homura is indeed from another timeline. Now the question is, is it a parallel timeline, or is it the future? If she is indeed the cat Madoka is holding in the OP, then does Kyubey begin the cycle at some point in the future, and Homura is somehow wished into having her soul taken from the cat and she gets a new body to use or something?
For Homura, I think she is from the future, and that it most likely is that she was friends with Madoka and Sayaka and Hitomi possibly even, before something happened and the witches came about.
Homura's weapon? I almost want to say War itself. Think about it from the first episode, she was attacking Kyubey with balls of energy, she had a grenade in her shield in this episode, and she was using a gun when she killed Kyubey. I think her weapon is actually her shield, and it is able to pull weapons from any time past, present, or future.
Kyubey is actually an incubator, so it would seem instead of calling him a garbage disposal system, we should call him a garbage compactor. He collects the sins and of the magical girls and concentrates the dark powers.
Another thing about Kyubey we learned, is that he has multiple bodies, which actually makes sense. When Sakura was introduced, Kyubey mentioned that he had called her to come take over the area that Mami was leaving behind. Now, how is he supposed to call her when, at least telepathically, you have to be within a certain range? Singlemind>>multiple bodies. This also shows why he went and ate the body that was left after he was killed by Homura. That body still contained whatever grief seeds it had taken in, as well as any possible evil that the evil bastard has normally.
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