Flavonoids such as epicatechin have been shown to reduce the risk of heart disease, since they act as anti-oxidants and thus reduce cholesterol levels. They are also responsible for the health benefits attributed to the consumption of tea and red wine. However, only in dark chocolate (> 70% cocoa content) flavonoids are present in sufficient quantities for these effects to be felt. There is also some evidence that flavonoids may reduce the risk of cancer. Another study pointed to a reduction of blood pressure, but only when consuming 100g of chocolate per day -- amounts which are likely to cause other problems outweighing the benefits!
Stearic Acid is a saturated fat, and makes up one third of the fat in chocolate. Unlike other saturated fats however, stearic acid appears to not increase cholesterol. A further third of chocolate fat comes in the form of a monounsaturated fat called oleic acid, which also does not increase cholesterol. Thus the fat in chocolate is not as harmful as one might think.
Theobromine is the defining chemical component of cocoa, which gives it its bitterness. It is a stimulant, but not as strong as caffeine.
Caffeine is also present in chocolate, but one would have to eat a couple of 100g bars of very dark chocolate to get anywhere near the amount of caffeine present in one cup of coffee.
Tryptophan is an amino acid from which the body makes serotonin, a messenger in the brain. High levels of serotonin are usually associated with an elevated mood. However it is not clear whether the amounts of tryptophan present in chocolate can really be said to cause a measurable change in mood.
Phenylethylamine is an amphetamine, and is responsible for chocolate's reputation as an aphrodisiac. As with tryptophan however, it is not certain whether the levels of phenylethylamine are sufficient for a definite physiological effect.
Anandamide is a cannabinoid -- it targets the same regions of the brain as cannabis. The quantities involved however, are once again very small, so that one is much more likely to be sick than high after consuming enough chocolate for anandamide to have an effect!
Sugar is the other main ingredient of non-milk chocolate besides cocoa. Hence a 70% bar can be thought of as 30% sugar. Sugar does not have many health benefits, and indeed was subject of a report commissioned, among others, by the World Health Organization in 2003 which recommended a low intake of sugar. The adverse effects of sugar are damage to the teeth and high calorie content.
Popularly, chocolate has also been linked to acne and hyperactivity. In both cases however, there is little scientific evidence to support these beliefs. The connection between chocolate and acne might partially be explained by an observed correlation between acne and milk consumption, making it possible that milk chocolate might cause acne.
If chocolate is consumed in moderation -- perhaps 10 or 20g a day -- the beneficial compounds such as flavonoids outweigh the negative effects of the sugar and fat. This holds particularly for dark chocolate. Describing chocolate as a ``health food'' would go too far, but it certainly deserves a better reputation than it has had in the past.