A few recent papers...
The issue of Nature Reviews Genetics from which I pulled the Homeobox genesis article actually contains a whole series of articles focusing on evolution of the body plan. Here's a brief taste of the good stuff found in the journal:
Garcia-Fernàndez J (2005) The genesis and evolution of homeobox gene clusters. Nature Reviews Genetics 6:881-892.
The crucial function of homeobox genes in patterning the body has been appreciated for decades. This article pulls together existing data to explain how the current clustered organization of Hox genes, and that of the related ParaHox and NK clusters, came about, the forces that preserve gene clustering and the contribution of Hox, ParaHox and NK genes to the major evolutionary transitions in animal body plan.
Pearson JC, Lemons D, McGinnis W (2005) Modulating Hox gene functions during animal body patterning. Nature Reviews Genetics 6:893-904.
The function of Hox proteins in axial patterning and morphological evolution ultimately depends on the effects of these proteins on downstream targets. This article reviews four important lines of research into Hox function - including work to identify the nature of Hox targets and define the structure of target enhancers, and the recent realization that Hox gene expression might be modulated by conserved microRNAs.
Peel AD, Chipman AD, Akam M (2005) Arthropod segmentation: beyond the Drosophila paradigm. Nature Reviews Genetics 6:905-916.
Genetic studies of Drosophila melanogaster have laid the foundations of our understanding of axial development. But just how universal is this fly model? The growing number of experimental methods that have become available for other arthropods is revealing a surprising diversity of pattering mechanisms, and allows us to formulate a model of how segmentation mechanisms might have evolved.
Martindale MQ (2005) The evolution of metazoan axial properties. Nature Reviews Genetics 6:917-927.
Multicellular animals come in many shapes and forms but they owe their body organization to the emergence of three design features - the anterior-posterior and dorso-ventral axes, and the three germ layers. Morphological and, more recently, molecular analyses on four basal metazoan taxa have begun to reveal how such features emerged and evolved, although a consensus model will depend on a stronger phylogenetic framework and a broader sampling of informative taxa.
Keep that all in mind next time a creationist tries to tell you that evolution is superfluous, or that Intelligent Design has a research plan.