GRASS (the Geographic Resources Analysis Support System) is a GIS (Geographic Information System), image processing system, graphics production system, and spatial modeling system - all rolled into one.
Emdros is a corpus query system for storing and searching linguistically annotated text; all linguistic levels of analysis are supported, including phonology, morphology, etc.
Checky is a document validation and analysis extension for Firefox, Mozilla, and Netscape; provides a UI to many free and commercial online validation and analysis services.
SoundRuler is a project created for acoustical analysis, graphing, and teaching; interactively recognizes and measures about 35 temporal and spectral properties of each pulse within each call in a file.
cingb is a project to write an emulator for all kinds of platforms; includes a debugger for step-by-step analysis of programs and might be also interesting for educational purposes.
SAGA GIS (System for Automated Geo-scientific Analysis) is a geographical information system (GIS); supports grid data like digital terrain models and satellite images, vector data, and tables.
Xrefactory provides code completion, source browsing, and refactoring functions for Emacs and XEmacs; based on full pre-processing, parsing, and static analysis.