"Functional" foods have no official definition or regulation at the moment, but the FDA is hoping to change that soon, giving both manufactuerers and consumers some guidelines to go by. Functional foods are those that have something extra added to them that promises "a special [nutritional] punch," one which may or may not be backed up with solid science. For example, some products with herbs like ginseng and kava kava promise, respectively, to "energize" and "enlighten" - and because these things are directly attributed to the two herbs, that makes them "functional" foods. The functional label doesn't just apply to herbs, however. It applies to cereals that are fortified with extra nutrients, or juices that have calcium added to them.
Right now, adding extraneous nutrients to foods is a huge trend in the food processing industry. Consumers are looking for quick fixes to getting all the nutrition that they need, so when they're offered a soda with calcium added, they're going to opt for that over the regular product.
Calcium, of course, is not really the biggest problem. The FDA is more concerned with the companies that hint at claims of increased intelligence, stamina or energy, things that are difficult to prove and can be confusing for consumers. The companies themselves say that as long as their foods meet the existing food safety standards and the ingredients themselves are considered safe, they should be able to continue on as they are doing.
We'll have to wait to see what restrictions, if any, are implemented, but it seems likely that there will at least be some. After all, we live in a world where toy superman costumes come with warnings that "cape does not enable user to fly," so it is reasonable to assume that we will also see some sort of warnings associated with "functional" foods.

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