Recommendations of software that we use. ...under construction...
Free Software
LibreOffice - No matter what operating system you are using. If you use any spreadsheets, word processors, or putting together presentations, you should be using LibreOffice. It has come a long way and now I use LibreOffice regularly. I have argued that it be promoted by the university as a free alternative for students to use instead of having them spend a lot of money on Microsoft Word, Excel and Power Point. Also, for presentations, don't worry if the computer you will be presenting on has the software installed. Just save your presentation as a PDF and go from there.
Linux Mint - I used to dual boot between Linux and Microsoft but now I am only running Linux Mint on my office computer. I've been using Linux since the 2.0 kernel in one form or another and it is amazing how far it has come. Linux Mint is impressive both in how easy it is to install and use and the resources that are available.
Mendeley Desktop - If you are a scientist you have folders of PDFs of various research journal articles on your computer. Mendeley is a great way to organize and manage them.
Texmaker
Rstudio
PERL
Tomboy Notes
Inkscape
Okular
Audacity
SageMath
Proprietary Software
Geneious - Geneious is a workbench for manipulating DNA sequence data. It combines many different tools (aligning, assembly, primer design, plasmid design, etc.) into one central interface and can work with genomic scale data. There are also a growing number of plugins that interface with popular DNA software in addition to Geneious' own algorithms.
Mathematica - If you can afford it, Mathematica is a truly impressive powerful workhorse for working with mathematical equations and visualizing data. I use it as a symbolic calculator engine because it save me a lot of time and prevents mistakes. When I first used it I was working on solving the eigenvalues of matrix of partial derivatives from a complex four dimensional dynamic system. I was doing this by hand with Laplace expansions and it took me days to work out and double check everything. I heard about mathematica, downloaded a free trial and tried it out. In literally minutes I had the same answer that had taken me days to arrive at before---I was sold. However, I feel that they are beginning to price themselves out of the market; especially considering free alternatives such as SageMath (that is nowhere near Mathematica's functionality but is gaining ground) and R (for data visualization).