There is some evidence that suggests that coffee is associated with a decreased risk of Type II diabetes and colon cancer. It can also help with weight loss, and with motivation to exercise.
Source(s):
http://mayoclinic.com/health/coffee-and-health/AN01354
One of the original research articles: http://www.ncbi.nlm.nih.gov/pubmed/15713963

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There are many studies that show that coffee and the caffeine therein provides several potent health benefits. An American study showed that caffeine can help block the damage that cholesterol could otherwise cause the brain, thus preventing dementia and Alzheimer's Disease. A Harvard study from the 1990s also suggested that those who drink coffee are less likely to commit suicide, due simply to its stimulant effects. Perhaps the most convincing of all is a 2007 study that concluded that coffee could prevent type-2 diabetes and certain cancers. Researchers also concluded a few months ago that coffee does not contribute to breast cancer, as had been previously believed.

Coffee gets a bad rap, and while some people get jittery from the stuff, it looks like drinking a few cups a day can be pretty beneficial.
Source(s):
http://latimesblogs.latimes.com/booster_shots/2008/10/caffeine-probab.html
http://news.bbc.co.uk/2/hi/health/7326839.stm
http://www.hno.harvard.edu/gazette/1996/03.14/CoffeeWontGrind.html
http://www.reuters.com/article/healthNews/idUSCOL15953520070501

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