Celestia, a space simulator on a desktop. Learn about astronomy. Open source. Available for Linux, Mac OS X, and Windows.
Celestia: Home
GCompris, a suite of educational software for geography, math, reading, science, and even games. Designed for children ages 2 to 10 years old. Open source. Available for Linux and Windows.
[Free Education Software GCompris]
jMemorize, a Java-based flash card application using the Leitner system. Features categories, stats, and more. Open source. Available for Linux and Windows.
Free Educational Software
Little Wizard, a software development platform designed for elementary school children. Learn the basic principles of programming. Open source. Available for Linux, Mac OS X, and Windows.
Little Wizard's Home Page
Multiplication Station, a grid-themed mathematic education application. Open source. Available for Linux, vMac OS X, and Windows.
Multiplication Station
Stellarium, a virtual space observatory. Open source. Available for Linux, Mac OS X, and Windows.
Stellarium
Tuxmath, a sort of "Missile Command"-style game played by solving math problems. Features Tux!

Open source. Available for Linux and Windows.
Tux4kids » Tuxmath » Home
Tux Math Scrabble, a "Scrabble"-style game involving mathematics. Open source. Available for Linux, Mac OS X, and Windows.
Tux Math Scrabble | Get Tux Math Scrabble at SourceForge.net
Tuxtyping, a game-style typing tutor. Open source. Available for Linux and Windows.
Tux4kids » Tuxtype » Home
Check out the SchoolForge.net site. It provides information on open source applications for students and teachers. In addition to learning apps, there are also applications for administration, course management, development, planning, and more.
Education Software for Schools: Free Software, Open Source | School Forge 