matplotlib-0.87 is out. Although a simple bump should be enough, I put a different ebuild for it in the Gentoo Scientific overlay in http://gentooscience.org/browser/overlay/dev-python/matplotlib. It contains a mplot3d USE flag to plot 3d, and adds a user guide if the doc flag is enabled.
matplotlib-0.87.2 was bumped in portage. Is there a reason not to include the changes fron the one in the overlay mentioned in the previous comment (namely 3d and wxpython)?
For 3d: I have no idea what the state of the tarball (http://matplotlib.sourceforge.net/mpl3d.zip) is. Is it alpha/beta/stable quality? Is it going to change in the future (the tarball is not versioned, so any change to it will cause digest failures). Is mpl3d useful without matplotlib (if it is it should be a separate package)? Is the patch to matplotlib in upstream's version control system? If not, why not? For wxpython: when I last tried this I ran into a couple of wxpython bugs I did not have the time to fix, and I am hesitant to add something I cannot test reliably. Also there were some fun bugs involving slotting iirc that needed further investigation (matplotlib has to keep working if various slotted wxGTK versions are installed/uninstalled).
For 3d: I did some digging in the matplotlib mailing lists, I found: http://sourceforge.net/mailarchive/message.php?msg_id=15110321 which states mplot3d is in their svn repo. So it should make it next version, and there is no need indeed to include for this one. For wxpython (wxpython-2.6.1.0), I tried only one version, I did not know about these slotting problems. It has been fairly stable for the very few times I have used it. There is one last minor extra about the ebuild in that overlay: it fetches and install a pdf user guide if the doc flag is enabled.