Maybe I missed it because it was late, but does anyone out there know the story I was thinking of? Here's my description from yesterday:
In the short story, written from the first person, a computer scientist describes an experiment he's performing. He's created a simulated world inside a computer, and in that box "people" who appear to display self-awareness are born, grow old, and die. The scientist notes with amusement that these simulated people have begun to speculate about his existence, some believing in a creator, and others professing atheism. The believers think that there is a "heaven" and a "hell" afterlife, and the scientist considers the possibility of setting up two more computer boxes connected to the original. The believers would have their program transferred to the "heaven" box after they "die," and the rest would go to "hell." He doesn't end up doing it, but the speculation is still there.
I really thought it was in "The Mind's I." The only other book I can think of where I might have read the story is "Mathenauts" edited by Rudy Rucker; my copy of that is also in storage.