I think, just like most things, moderation is key. A cup of coffee to help get you up and motivated is awesome. Just like COJock said though, be aware of what's going into it. A huge amount of calories and sugar can be added by what is put into it.
A small amount of caffeine is great. I have read many studies about increased metabolism, improved cognitive function, increased energy, etc...
The worst thing I have read about it is too much coffee (or caffeine) can seriously increase cortisol hormone levels in the body, which is also released during very stressful times. Cortisol can seriously effect weight and mood. It is often times called the "death hormone" by many doctors because of its detrimental effects to the body.
So like everything else in life, it's all about moderation. Give me a cup of black coffee before a workout any day! But I will take just one please, lol.