What would you like to ask the Creator when you get the chance to stand before Him/Her/It for the first time?
Why did you leave sinuses ( I probably misspelled that) in the final design plans?
That little piece of paper I found with the words ‘Roxell Roxell Bowshot’ on it, what was that about?
Why did you see fit to have me born and live in the late 20th century in America instead of sticking me in, say, the 1400s in Iceland?
Are all religions right, or just one? Which one? Why didn’t you make this clear?
Don’t you get bored?
What’s the deal with the rabbits digestive system? Were you tired that day and didn’t finish? Did an incompetent assistant design the rabbit?
Bob
Why do you have people believing there is some kind of “religion”?
Then I would promptly ask for the ingredients in which everything was created, and sell it to China, before Clinton does.
why do we have lips? wouldn’t a hole do it for eating purposes?
(not THOSE lips perverts)
What were you thinking?
Where did you get the idea for the Platypus?
[ul]
[sup]Where’s my car keys[/sup][/ul]
Why did 9/11 happen?
Why even bother with the dinosaurs, and just skip right to us ?
Why did you trick people into believing you exist. What do you mean, what do I mean by “you”?
Could You microwave a burrito so hot, that even You couldn’t eat it?
Also, what’s up with scrotum sweat? Surely You must have realized that there is little opportunity for evaporative cooling down below?
Why do my ears and nose keep growing when the rest of me doesn’t?
Why am I losing hair on my head, and gaining it on my ass?
Who shot J.R.?
I have a few (serious ones)
What happened to the colonist on Roanoke Island?
Who was Jack the Ripper?
Stonehenge?
I love history mysteries, and I can’t wait till he tells me the real answers 
I’m going to presuppose that all of the “great” mysteries become clear once we have crossed on to the other side, so, here’s my burning question concering the minutia of our daily existance:
Carrot Top??? WTF is that sh*t all about? Please, Oh Great Diety, why, why, why?
Why did you allow head lice? What possible function do they serve? Surely they don’t make you happy?
When/if—ever you get this answer, please come immediately to the
SDMB and let the rest of us know! Mangetout, okay? 
(meanwhile…I’m still pondering my quest)(yon)