Veusz: A scientific plotting and basic fitting application
An excellent freeware which can plot most kinds of graphs. Best part is its good fitting tool.
Veusz homepage
PHREEQC: Aqueous Geochemical Calculations
A good program to simulate aqueous chemistry. The software can be accessed through Python via IPHREEQC COM application on Windows or using PHREEQPY library.
PHREEQC 3 homepage
Cherry Tree: A heirarchial note taking application
A good free software to organize the daily work. The beauty of the software is its ability to link to files, add snippets of code, add tables, add bookmarks for certain nodes and exporting into pdf (very good rendering).
Very useful to organize literature data.
Cherry Tree homepage
Notion: Productivity tool
A good software for note taking, tracking tasks and much more.
Notion homepage
Medusa: Chemical Equilibrium Diagrams
A good free software to generate various kinds of chemical equilibrium plots.
Medusa homepage
GSAS II: Tool to analyze XRD data
A user friendly python-based free software for analyzing powder and crystal XRD data. The software can be used for Rietveld refinement. It is not a peak search/matching tool, so, XRD pattern files for minerals are to be downloaded from other databases such as ICSD.
GSAS II homepage