I just developed a new "static" 3D phylomorphospace function; i.e., one that uses R base graphics to simulate three dimensions in a static plot, rather than the rgl library. The advantage of a static plot over a (much more impressive looking) spinning dynamic plot is that it is much easier to modify the plot using base graphics, and it can be exported in standard formats or combined with other plots. Code for this new version is here. The method uses scatterplot3d internally. It is also in a new phytools build (phytools 0.3-40) which can be installed from source.
Here's a quick demo of each method and the different products they create:
Loading required package: phytools
> # simulate tree & data
> # first, method="dynamic" (the default)
> movie3d(xx,duration=20,dir=".",movie= "phylomorphospace3d")
Will create: ./phylomorphospace3d.gif
Obviously, the dynamic plot makes it a lot easier to see depth in the 3D plot; but the flat plot has the advantage of being something that we can more easily print to a page or combine with other R graphics.