After waiting in the JFK immigration line for over an hour, I saw that they have kiosks (Global Entry) for trusted travelers. Since they only had 7 immigration officials working the 16 US citizen queues, it seems like applying for Global Entry program would be a nice shortcut.
Nowhere on global entry's front page, which has a handy "Apply Now!" link, does it say that Global Entry has a 100 USD application fee. Only at the end of the lengthy application process does it tell you that you have to pay them 100 USD in order for them to save money.
It's understandable to have a fee to dissuade people from filing junk applications, however they should refund the fee upon success since they'll be saving immigration officials processing time. Otherwise it looks like they're under-staffing lines in order to get people to pay for Global Entry.