It's not referencing The Venture Brothers.
They're both referencing Are You There God? It's Me Margaret by Judy Blume. Your girlfriend was right.
I wouldn't be suprised if the Venture Brothers usage triggered this though. Seems too suspicious to be completely coincidental.
Not really. I've seen references to the title since I was a kid. If you have Firefox 3, type "are you there god it's me," and you get a huge dropdown of choices.
Hell, since posting the link this afternoon, I went to the bookstore and spotted a copy of Are You There, Vodka? It's Me, Chelsea by Chelsea Handler.
It's a common enough reference that it's actually getting kind of passé.