I had to take one of these upon being hired by dot.gov, even though I had done the same work for several years. Anyway, the questionaire asked me about 8 times if I was afraid of the dark or if I hated my mother. Seemed rather useless to me.
2 years after being hired, they claimed that they had "lost" everybody's security clearance information so they had to perform an invasive security check on all the people in our department (probably a post-9/11 overreaction). At any rate, they actually did call my 3 references and did a check on my credit. I have no idea why they checked my credit, as I don't handle anything financial.
6 more days and it's all behind me - I'm returning to the private sector.
The various gov't agencies use the credit check as an indicator like any other. If you have a really bad credit history (late payments, judgements etc.) then you are more of a risk than someone who pays their bills on time, doesn't overextend themselves and so on.
Higher clearances will be turned down if you have an unpaid cell phone bill in the past. Has nothing to do with weather you work with money, it's how you comport yourself with credit and responsibility.