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David Manthey's Orbital Viewer freeware rendered atomic and molecular orbitals with point plots, polygon surfaces, ray tracing, stereo views, cutaways, animation, and VRML output on Windows systems from the 1990s and early 2000s.
Robert Scharein's KnotPlot site grew from PhD work into a sprawling visual laboratory for mathematical knots, links, stereoscopic images, and topology software.
DPGraph is a surviving late-1990s mathematical visualization program written entirely in assembly language, capable of interactive graphs extending well beyond ordinary three-dimensional plotting.