molsKetch is a KDE 4 2D molecular structure editor.
ZEM is an editor of molecules using Qt4.
XDrawChem is a Qt3-based application to draw molecular 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
Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas using Qt4.
BALLview is a 3D protein visualisation program using Qt4
Zodiac is a molecular modelling suite for computation, analysis and display of molecular data using Qt4.