The cross described is called a "dihybrid cross," i.e., with two genes involved. The genotypic ratio for such a cross is 9:3:3:1, or the 16 possible combinations Chad mentions. After Mendel figured out the way single traits were transmitted, he wondered what happened if individuals differing in two traits were crossed.
The dihybrid cross was the way he established his second law of heredity: the principle of independent assortment. Mendel, of course, didn't call his box a "Punnett Square," since this wasn't developed until later.
If you look at the Punnett Square on page 14, you'll note the genotype in the lower right box should be "bbee," not "Bbee," as shown. (It can't be Bbee, since there is no dominant B allele in either parent.) The phenotypes are correct. A corresponding change to clarify would be to make that box a different color from the other 15 boxes. Then you'd have nine black boxes, three yellow, three brown, and one of the "new" color. With these slight changes, the expected 9:3:3:1 ration is clearly demonstrated.