Origins of novelty
Perhaps one of the most striking features of macroevolution (i.e., differences between taxa at the species level or above) is the origin of new features (organs, functions, forms, body plans). Because differences in the body plans between Phyla (and especially differences between Kingdoms!) have arisen by the accumulations of changes over great expanses of time, these changes are very difficult to reconstruct.
But there are also significant differences between more closely related organisms where the clues to their origin are more likely to have been preserved. Unless something very "special" occurred in the Precambrian and in the Cambrian, studying the changes involved in the evolution of differences between closely related taxa, should provide insight into the kinds of changes that accumulated and mechanisms that operated to distinguish distantly related groups.
In the two pages that branch from this one, we will discuss firstly the kinds of macroevolutionary changes that have occurred (especially at the morphological level) that could be significant with respect to the evolution of "novel" features, and secondly the kinds of mechanisms that could have produced these changes. Keep in mind, of course, that the evolution of "novelty" must occur by modification of pre-existing characters.
Books on the evolution of form
Rudolf A. Raff. 1996. The shape of life: Genes, development, and the evolution of animal form. The University of Chicago Press, Chicago. [See chapters 7-10 especially; on reserve in Bobst Library.]
Stephen Jay Gould. 1977. Ontogeny and phylogeny. The Belknap Press of Harvard University Press, Cambridge, Massachussetts. [See especially chapters 7-10; on reserve in Bobst Library.]
Brian K. Hall. 1992. Evolutionary developmental biology. Chapman and Hall, London. [In Bobst library.]
Stephen Jay Gould. 1989. Wonderful life: The Burgess shale and the nature of history. W. W. Norton, New York. [In Bobst library.]