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.
The Mnemosyne software resembles a traditional flash card program to help you memorize question/answer pairs, but with an important twist: it uses a sophisticated algorithm to schedule the best time for a card to come up for review. Difficult cards that you tend to forget quickly will be scheduled more often, while Mnemosyne won't waste your time on things you remember well.
LON-CAPA (The LearningOnline Network with CAPA) is a learning content and course management system. It offers an underlying shared content pool from which instructors across departmental and institutional boundaries can assemble granular learning content for their courses. It has strong assessment capabilities, both formative (homework and in-class using wireless PDAs) and summative (online and bubblesheet exams), with a one-source multiple-target strategy for the content. It offers students portfolio space in which they can stage materials for submission to projects, and provides a number of tools for synchronous and asynchronous student-student and student-faculty communication. LON-CAPA scales well with number of students, as load-balancing is possible across the whole network of servers at participating institutions.
Foswiki is wiki software, supporting the editing of Web pages in an ordinary Web browser by end users. What makes Foswiki special is that it supports the embedding of active and passive macros that enhance the page content (e.g. with global or dynamic information) and allow end-users to build applications that store and process data in a structured manner.
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.
Diogenes is a tool for searching and browsing the Latin and ancient Greek texts published on CD-ROM by the Packard Humanities Institute and the Thesaurus Linguae Graecae. It comes as an easy-to-install stand-alone application for GNU/Linux, Mac OS X, and Windows, based on the Firefox browser (i.e. Xulrunner). Alternatively, it can be installed by a network administrator as a server on a local network, and users then access it via an ordinary Web browser. There is also a command-line tool which can optionally format output as LaTeX instead of HTML.