I'm aware of quite a few sites out there (e.g. morphobrowser, morphosource, nespos, evans) but I'm always looking for more.
In particular, I'm looking for ones that have CT scans high quality enough to do research with...i.e. the Digital Morphology Museum, KUPRI has a TON of amazing primate CT scans for free download. However, they're not particularly high quality, making it difficult to use for anything other than gross geometric measurements and/or teaching.
If you need any micro-CT scans of human teeth (i.e. incisors, premolars or molars), let me know. Got a 15incisors, 60Pms and 60Ms scanned at 13.59um resolution that I'm willing to share.
Maybe also check the Virtual Anthropology project (University of Vienna), they might have some free data sets of skulls.
Contact universities (departments) or museums with CT-scanning facilities (e.g., London Natural History Museum, Frankfurt Senckenberg, Berlin Natural History Museum and many others) and collections of extant and extinct mammals. I have made good experience with colleagues!
there are some sample data sets at this tutorial for the 3D slicer software:
http://openpaleo.blogspot.de/2008/12/3d-slicer-tutorial.html
http://www.ohio.edu/people/witmerl/lab.htm
also http://digimorph.org/
Another place I just found to download scans and surface files
http://phenome10k.org/
If you are interested on non-human primates CT scans, there's a bunch of them free to be downloaded (prior registration) on the Digital Morphology Museum of the KUPRI (Kyoto University Primate Research Institute)
http://dmm4.pri.kyoto-u.ac.jp/dmm/WebGallery/index.html
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