The ending of Mawaru Penguindrum had a lot of ambiguous symbolism.
My first impression was that the writer had no idea how to resolve the fundamental questions of the plot, and thus had to throw out completely unresolvable symbolism in order to fake an ending. A few of my driving questions throughout the series were as follows:
A recurring motif of the show is that the main character would get possessed by a penguin hat, and pull one or two characters into a kind of alternate reality where they were handcuffed. To what degree was this a hallucination? Likewise, Penguins 1, 2, and 3, plus the additional penguin, were important characters who were not visible to most people in the show. To what degree were they hallucinations, and to what degree were they paranormal?
Were there any forces in the story that were godlike, in that they were both powerful and capable of passing judgement on mortals? In particular, at the end of the show, it seems that two boys sacrificed their mortal lives for the sake of two girls. Was this a sacrifice made to a god or other cosmic power?