The right tools can help you to save time and energy. And both are crucial during a PhD.
Choose colors for figures
Taking equidistant colors in the HSV color space is no solution for finding a set of colors that are perceived as equidistant. This post describes what’s wrong with HSV and what we can do about this.
I want hue
Hue, Chroma, Lightness colorpicker for data
LibreOffice or Apache OpenOffice
Because for a small document or a presentation, What you want to get is what you see on the screen. It support tracked changes and comments, it is easy to add formulas and to export in *.pdf. A good free alternative to Microsoft Office.
Texstudio (LaTex editor) and MiKTeX (typesetting system)
MiKTeX ask users whether they wish to download packages requested by the current document, and that is fantastic when, like me, you learn a language by copying and pasting several pieces of code found on the web.
Mendeley is a free reference management application. It can be used with Microsoft Word, OpenOffice, LibreOffice or LaTeX (BibTeX export).
TortoiseHg is a Mercurial revision control client. Very useful for collaborative work.
Inkscape is an open source vector graphics editor. It is very easy to use.
Code::Blocks, Qt Creator, Arduino software
Three cross-platform to use your C/C++ abilities: Code::Blocks to learn, Qt Creator to make an user interface and Arduino software to use the famous open-source electronics prototyping boards.
Python has a growing audience, and is a serious free alternative to Matlab with the librairies NumPy, SciPy and Matplotlib.
Matlab & Simulink
The first software in this list that is not free. Simulink seems to have no serious free equivalent and Matlab has a strong academic and industrial community, and is purely made for scientific computing (and this is one of the major drawback). I like particularly the profiler tool.
Some links for matlab:
Fixed-step Ordinary Differential Equation solver (ODE)
Rainflow Counting Algorithm
CVX for Disciplined Convex Programming
SolidWorks and CATIA
These are definitely not free (Dassault System). But the first one is a powerfull CAD program and the second one is a very large software suite for CAD, CAM and CAE.