QMForge reads output from various quantum mechanical calculations and provides tools for analyzing these results. Specifically, population (Mulliken and C-squared), fragment, and charge decomposition analyses are available.
See https://qmforge.net for more info.
PyMOlyze is a graphical program to analyze the results of quantum chemistry (HF/DFT) calculations. Features include various population analyses, fragment analysis, monitoring structures during an optimization, and a simple, but powerful, XYZ editor.