Jean Jacques Hublin has a commentary [1] in the current issue of Nature, about making fossils available for scanning, digital replication, and ultimately hopefully open dissemination. As Hublin points out, it’s a bit ridiculous that a fossil is a rare enough thing as it is, but even after their discovery, fossils “can become unreachable relics once they are in storage.” Fortunately, Hublin goes on to point to online collections that are available to anyone interested. Somewhat ironically, the article about free-ish data is behind a paywall, so here are the resources Hublin describes:

• The Ditsong CT Archive, created by the collaboration of Hublin’s group at Max Planck and the Ditsong (formerly Transvaal) Museum in South Africa, which contains digitized hominin fossils from the site of Kromdraai (see also [ref 2]). Check out the type specimen of Paranthropus robustus, from this site, above!
• You can download CT scans of the Skhul V early human fossil from Morphosource, thanks to the Harvard Peabody Museum.
• Wanna see the the oldest possible animal embryos, early humans, insects, and other crazy fossils? Check out the European Synchrotron Radiation Facility’s microCT database.

In addition to these sources, here are 2 other datasets that are pretty badass:

• The American Association of Orthodontists Foundation has published several sets of X-rays from longitudinal studies of craniofacial growth. It’s quite a remarkable and useful collection for both research and teaching.
• [2026 update] The Human Fossil Record is a large repository of CT scans and 3D models of apes and fossil hominins from a number of institutions. The 3D viewer mode is great and allows you to take linear measurements as well as 3D coordinates. The site also includes information for how access original fossil data from their respective institutions. Great stuff here!

I haven’t had much opportunity to look into these datasets Hublin pointed out, but they look promising. If you know of other good resources, please do share!

References
[1] Hublin, J. (2013). Palaeontology: Free digital scans of human fossils Nature, 497 (7448), 183-183 DOI: 10.1038/497183a

[2] Skinner MM, Kivell TL, Potze S, & Hublin JJ (2013). Microtomographic archive of fossil hominin specimens from Kromdraai B, South Africa. Journal of human evolution, 64 (5), 434-47 PMID: 23541384