One standard question was brought up on another thread that has gone on far too long asking a very old, very valid question about why God allows innocents, especially children, to suffer (this was not the exact context of the question, but it does hit on the high points).
I have wrestled with this question for years, until I realized that, in my personal opinion, it has to do a lot with what God is teaching us. Our capacity to kill is matched only by our capacity to heal; in the same years that have seen us develop weapons of mass destruction that were unforeseeable just a century and a half ago, we have created marvelous vaccines and medicines that, literally, can do a world of good. Our funding, however, is persistently dedicated to destruction over healing (this problem is not unique to the US, it is a worldwide epidemic). I do believe that God COULD eliminate all of these problems with a wave of His hand, the reason He doesn't (again, my opinion), is the same reason that a parent fails to bail out an irresponsible teen; there are things we MUST learn if we are to grow.
I am sure that the pain, disease, and destruction that are so rampant worldwide, pain God deeply (far more, at least, than the sexual preferences of the guy down the street). But we as humans have so far to go, and so much growing to do. And God is teaching us how to do so.
Just my two cents,
Gideon MacLeish