gtk, Good toolkit. It is free, is actively being developed, has binding for lots or languages.

Mesa. A free implementation of OpenGL.

OpenGL. The official OpenGL site.

Pstoedit Converts PostScript files into several editable file formats.

GtkGlarea Gtk+ wrapper for opengl.

Geomview Visualization of geometric objects.

MathGL3d mathematica object interactive viewer.

Mupad Computer algebra system. I think is very complete; what i hate is it's interface, and the c-like language.

Octave Another computer algebra system. This one is GPL. I haven't look at it (yet), but again, really dislike the language.

Yacas. The beginning of a free computer algebra system. Very similar syntax to mathematica. I find it very promising.

Mathematica I think it's one of the best software systems made.

fte. This is an excellent text editor. It is FAST, does syntax coloring for several languages.

ddd. A front End to gdb.

Glade. A gtk+ user interface builder. It has save me several hours of boring work.

pdl A numerical language for perl.

IDL The Interactive Data Language.