I prefer to have paper copies of anything relevant. Which is more the 'analog' way :)
In addition I'm storing anything related to my topic - preferably in the .pdf format. Where a document is not already available digitally, a good scanner helps. Thus some mass storage device.
Not to be forgotten: a backup device.
Some database may come handy: to have a digital catalog of the materials available. Depending on the number of documents (I personally have GBytes of significant documents). I have to admit that I'm thinking about creating such a catalog but have not yet started with that, thus relying on the capabilities of search tools.
The text editor of your choice. For me it is still MS Word - a question of convenience and familiarity. But any other reasonable text editor (eg. open/libre office) might do as well.
Beyond that? The browser of your choice - just to aquire all the materials via internet search etc.
Among the tools to increase research productivity, the one to me that proved to be the most useful was a proper reference manager. I personally suggest Mendeley (https://www.mendeley.com). It is a nice tool that gives you some cloud space to store publications, tag and categorize them, save annotations and comments, and automatically handle bibliographies in the papers you write (Mendeley has MS and Open Office plugins, besides the built-in LaTeX support, and supports many citation styles, like IEEE, APA and AMS). There is other software in this category, and you can find a comparison in https://en.wikipedia.org/wiki/Comparison_of_reference_management_software
Besides, another tool that helps to organize your ideas before starting to write a report, research paper or anything else, is mind-mapping. It is just a type of diagram to visualize ideas graphically. However, it does an amazing job if the idea/problem is complex, and you need to "divide to conquer". Please see https://en.wikipedia.org/wiki/Mind_map for more information. In the link there is also a software comparison, but you can always resort to the good old pencil and paper.