Open source science software has a lot to offer the scientific community. This is a far from complete list of open source science software that I’ve found useful in the past.
If you’ve done any scanning probe microscopy (SPM), it’s likely you will have come across Gwyddion. I’ve found Gwyddion can open pretty much any SPM file type I’ve thrown at it, and it has some excellent flattening and editing tools.
ImageJ is a Java-based imaging suite. Being based on Java means that it can work on pretty much any system. The vanilla version is probably plenty for most people, but you can also extend it with plugins. I’d actually recommend FIJI (Fiji Is Just ImageJ), a distribution that comes bundled with a range of useful plugins.
If Inkscape is an Open Source replacement for Adobe Illustrator, then think of Paint.NET as an alternative to Photoshop. GIMP is probably the most well known open source image editor, but I’ve always found Paint.NET easier and more intuitive to use. Unfortunately, as far as I know, it is only available for Windows.
LaTeX is a typesetting tool, used for (hopefully painlessly) making beautifully typeset documents. In recent years Microsoft Word has advanced to the point that LaTeX is perhaps not as important as it used to be, however. That said, even if you only consider using it to write your thesis, it’s worth knowing that Latex is about.