The Wikipedia's page on it has an interesting origin[1]:

    The Oxford English Dictionary has published references going
    back to 1718 for “perfect storm,” though the earliest citations
    use the phrase positively, as in a “perfect storm” of applause.

It also notes that the phrase,

    is nearly synonymous with "worst-case scenario," although the
    latter carries more of a hypothetical connotation.

The phrase is relatively rare in normal British English usage, and it's usually used in the ``worst-case scenario'' sense. To me, the word `storm' brings with it a negative connotation, but I suppose it's logical enough, albeit a little strange, that it could be used to describe a positive set of circumstances.

[1]: http://en.wikipedia.org/wiki/Perfect_storm