Feeling confident of my current level of progress, I think it's worth pointing out that the entirety of my doctoral thesis work has been done using free, open source software. I wanted to write a quick overview of my system, explain where it falls down and give an honest appraisal of how it went.
Operating system: Ubuntu GNU/Linux
Word processor: LibreOffice [previously OpenOffice] Writer
Spreadsheet: LibreOffice [previously OpenOffice] Calc
Bibliographic manager: Zotero
Email client: Mozilla Thunderbird
Web Browser: Mozilla Firefox
Backup solution: Unison
This worked for me for the whole of my thesis work. I have to confess that I have started my (legally licensed) copy of Microsoft Word inside a Windows VM when I needed to submit a file (for a job application) in MS Word format and I wanted to be 100% sure that LibreOffice had converted it successfully. Most of the time, though, the convert to PDF option in LibreOffice is more than enough to ensure cross-platform format.
This could also be discipline specific. I don't know, for instance, whether specific lab software is available in free, open source versions. I somewhat doubt it.
Furthermore, it has not been a smooth ride. I class myself as very technically able and I have had occasions where an upgrade has totally broken my install. That said, I enjoy the challenge of knowing that I am wholly responsible for my computing and take pride in the setup and operation of systems over which I have full control. Has anybody else worked along these lines?
Featured image by okubax under a CC-BY license.