After Kalzium and kfilechemical, KDE has now be extended with kparts for 3D structure and spectrum display: Kryomol. It is written in C++ and licensed GPL. It supports several chemistry formats, among which quantum chemical formats like Gaussian03, NwChem and ACES, and 3D structures as MDL molefile and XYZ.
Egon Willighagen (Sat,) studied this question.