FlightGear Flight Simulator: free open-source multiplatform flight sim
Open Source Solid Modeling CAD
LDraw™ editor for LEGO® style digital building instructions.
rayshade and POV for Mathematica Export + view
3D .NET engine for Windows, Linux, Mac
PHIGS (Programmer's Hierarchical Interactive Graphics System)
Pear3DEngine is a modern and modular 3D development framework
1st 3D game engine built in C# for .NET, Visual3D Engine's predecessor