XDrawChem is a Qt-based application to draw molecular structures.
With Jmol you can view molecules inside your browser. All you need is java enabled in your browser.
The Gnome Chemistry Utils provide C++ classes and Gtk+-2 widgets related to chemistry.
This Windows™ software package - free for students, runs via wine on Linux - is in my opinion the best drawingapplication. It is really almost perfect and even supporting a 3D-viewer.
ChemTool is a GTK application for drawing chemical structures.
Open Babel is a project designed to interconvert between many file formats used in molecular modeling and computational chemistry. Since KDE4, Kalzium is using OpenBabel (2.1+) if you have it installed. It is used to calculate and display 3D-structures in a OpenGL-based moleculeviewer