If a company is selling a product labeled 100% whole wheat, but ther germ has been removed, it is violating FDA recommendations. The FDA uses this definition of "whole grain":
"# Question: What factors should be considered in determining whether a food is a whole grain?
Answer: Cereal grains that consist of the intact, ground, cracked or flaked caryopsis, whose principal anatomical components - the starchy endosperm, germ and bran - are present in the same relative proportions as they exist in the intact caryopsis - should be considered a whole grain food."
Unfortuantely, because these rules are only "guidance," the companies cannot be charged or punished by the government. However, consumers can voice their frustration and point out that they are violating government standards.
More info:
http://www.cfsan.fda.gov/~dms/flgragui.html