• Phoenix (Computer Interfaced Science Experiments)
• Step (An interactive physics simulator, part of KDE-EDU package)
• GeoGebra (A dynamic Geometry and Algebra Platform)
• KTurtle (A simple turtle graphics program using LOGO for children)
• Inkscape (An advanced vector (SVG) graphics editor)
• Stellarium (A planetarium for your computer)

Many of them are well known, except Step.  I want to therefore say few words about it.  This program will have a great role to play for physics education. An excellent platform for learning as well as teaching.  If you are a physics teacher or an educator, consider using Step.  Though the program needs several finishing touches (sometimes eats up resources while simulating complex systems), the author (Vladimir Kuznetsov) is ambitious and did a fantastic job.  Once this program is improved, it will be a classic tool for education in the high school and college level physics.

Geogebra also gives the same experience for mathematics.

These are all free software for education.  I encourage teachers to use them in the classroom, and students who own a PC must install GNU/Linux on their PCs and enjoy these applications among several others.