Hmm, I believe it was Robert Browing who said, "When God's in His Heaven, all's right with the
world." He was a 19th century poet and it's from a poem he wrote called "Pippa Passes" In the poem,
Pippa says the phrase because she is really happy with the world around her, no matter how cruel or mean the world
actually appears to be.
I think Matt Greenfield says that NERV uses it because it's basically stating the fundamental essence of the show
in which God or enlightenment is removed from the body. That is, God is in His Heaven; He is not here with us.
The leaf, is a fig leaf! Which means it's a Judeo-Christian symbol for original sin. You see, in the Bible, God
tells Adam and Eve not to eat from the Tree of Knowledge, but they do so anyway and when they eat from the tree they
learn right from wrong. They realise they are naked and cover themselves with fig leaves.
So in actual fact, the leaf represents humanity's fall from grace, but also humanity's knowledge (prefectly
depicted through NERV itself), which is being used to counteract God.
I learned the above, some from my friend Kate who's a whiz on Evangelion, some from what I read on the net, and I
believe the magazine "Anime Invasion" did an article on it too.
Hope it was helpful!
^_^v