So what does all this mean? There are an incredible number of ongoing experiments and clinical studies occurring right now that are looking into the pros and cons of coffee and its chemical compounds (see references below to get into more of the details). Just like anything else, we don't know every piece to the puzzle, but what we do know so far helps me to rationalize my 2-3 cups/day routine! :-)
Please note: I'm not a doctor, I'm a scientist! Always ask your doctor if you're not sure what the impact of coffee and caffeine will have on your system.