Harold Thimbleby, 2003 (revised 2011).
Gresham College 'Magic picture' talk (October 2003) lecture notes: PDF
3D web design: H. Thimbleby, "3D Creativity for the Web," The Internet in 3D, R. Earnshaw and J. Vince, editors, pp41-53, Academic Press, ISBN 0-12-227736-8, 1997.
Technical article: H. Thimbleby, I. H. Witten and S. Inglis. "Displaying 3D Images: Algorithms for Single-Image Random-Dot Stereograms," IEEE Computer, 27(10), pp38-48, 1994.
Algorithm in detail: H. Thimbleby, "An Equivalence Class Algorithm for Drawing Autostereograms," Software-Practice & Experience, 26(3), pp309-325, 1996.
General level article: H. Thimbleby and C. Neesham, "How to Play Tricks with Dots," New Scientist, 140(1894), pp26-29, 1993. (Sorry! But you'll have to register with New Scientist.)
Finally, see the article and resources in Wikipedia.
If you have an old Mac, this is a program I wrote to experiment with autostereograms. You'll need Stuffit to expand it — and OS9!
Whether you have Adobe Photoshop or not, read the very good documentation (in PDF) describing my plugin and its many features. The plugin is available.
Animated autostereograms: http://www.imm.dtu.dk/~uniaaa/MagicEye/MagicEyeAnim.html - Anton Antonov Antonov's web site, with pictures like this (generated in Mathematica), with acknowledgements to Lichtenstein's Shipboard girl:
Anton has also combined static and animated autostereograms:
If you have further links you'd like added, drop me an email.