Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
Peklo is a graph editor and an environment for visualizing and comparing different algorithms for some graph theoretic problems. Currently implemented are algorithms for maximum flows (including multi-commodity and balanced flows), minimum cuts, shortest path, minimum spanning tree, and maximum matching.
StatPlanet Map Maker is a program for creating interactive thematic maps and graphs. Data is read from an external file (.CSV) which can be easily edited. Customization options include specifying the zoom level, creation of selectable regions, changing the map colors, and adding country mouse-over text.
X-Plane is a flight simulator that reads in the geometric shape of any aircraft and then figures out how that aircraft will fly. It does this via an engineering process called "blade element theory", which involves breaking the aircraft down into many small elements and then finding the forces on each little element many times per second. These forces are then converted into accelerations, which are then integrated to velocities and positions. This gives X-Plane the most realistic flight model available for personal computers.