[aruanan]

Here's about the Hiroshima/Nagasaki bombing:

I heard that Nagasaki was an alternate, chosen after the primary target couldn't be located, and that the irony was that Nagasaki was one of the main Christian cities of Japan.

[annalex]

The source fo the first quote is Hiroshima and Nagasaki article in About.com. It does nto mention that theory, but indeed, more than two cities were chosen, and it looks like the ones with clear weather were the unlicky ones.