There's a load of interpretation on the main page right now. (see excerpt below).
I love this song because it's so funky (same for Elevation) in a Sly Stone kind of manner--but more so because it is about Sex and Spirit together.
For those who try to claim Bono as a Fundamentalist, this is one place where he is a bit more subversive, suggesting the feminine aspect of the divine.
love, Anu
from the main page
Some interpretations of "Mysterious Ways" indicate this song is also a retelling of the Salomé story in both the New Testament and Wilde's play. The song's "Johnny" could be John the Baptist, or it could be anyone. Bono's explanation to Niall Stokes in "U2: Into the Heart: The Stories Behind Every Song," leaves even more room for interpretation:
"'It's a song about a man living on little or no romance,' Bono says. 'It's a song about women—or a woman—but it's addressed to him.' Bono talks a bit about theology and about El Shadi—the third and least used name for God in the Bible, which translates as 'the breasted one.' 'I've always believed that the spirit is a feminine thing,' he says. 'Mysterious Ways' is not about a particular woman. It is about women in general, and the way they entrance—and often dominate—men."
Images of belly dancers during live performances seem to further link Salomé the dancer (and the song) to "Mysterious Ways." The sensual, almost hypnotic music of both tracks is enough to give away the common denominator in both songs—sex. Both of these songs speak to the compelling power of desire. That's something anyone can tell you, even without the Sunday school lesson.