Geotools
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One of the best free visualization tools that saved my life during structural geology. You can visualize folds and cross sections but the best feature is the stereonet where you can add strikes and dips!
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It is a software that is unfortunately not free but does offer a free trial. It is great for 2D and 3D visualization as well as editing DEMs and a plethora of other mapping tools.
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A free software for visualizing crystal structure and behavior. Definitely worth taking a look at during mineralogy.
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An open source software for thermodynamic modeling of phase equilibrium in thermodynamic systems in magmatic systems with the variables being temperature and pressure.
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An open source code that is implemented in MATLAB that can be used for determining the rheological behavior of dense pyroclastic flows and debris avalanche​, volcanic hazard mapping, and the simulation of tsunami, lava flows, and dense and dilute pyroclastic flows.
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ArcGIS/R/MATLAB
Hopefully you can get these three programs with your university because they're definitely worth it but definitely expensive.
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The one stop shop for coding with python. A must for coding.
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An amazing desktop software for the interactive visualization of plate tectonics.