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Not once have I seen a question from a religious SE site show up in the "Hot questions" side bar, and I've been keeping an eye out for over a year now.
Is it because the stack exchange network doesn't want to spark controversy by including religious questions? Personally I would love to see a hot question from Christianity.SE pop up every now and then.
The same applies for Mi Yodeya and the Islam and Hinduism SE sites. Why does nothing from there ever show up in the side bar?
Perhaps they are using an automatic algorithm to select the hot questions? In which case I would like to know why this algorithm is discriminating against the religious sites.