Okay, so lets review the final episode.

Madoka makes her wish, rewrites the laws of the universe.
Magical girls all around the world are free of the curse of the cycle.
Wraiths are about and are ugly faceless sand people looking things.

Homura was feeding kyubey cubes (that amussimngly, come from wraiths) atop a high building.

Edit: I just found this and its a great resource.
[hider=Timeline Chart][img]http://images.puella-magi.net/8/8a/Timeline_Chart.png?20110711110108[/img][/hider]