Following are some useful (and almost free) tools that will help you out during your PhD journey.

1. Dropbox: For saving all your work and materials, think about using a cloud-based app like Dropbox (has the best synchronization ability IMHO), Google Drive, Microsoft’s OneDrive, or Box, etc. Trust me they will save you a life when one day your PC is broken or you accidentally format your hard disk.
2. TeXStudio, Texmaker, LyX: For editing LaTeX documents, try TeXStudio, Texmaker, LyX (very friendly, highly recommended), etc. To easily share and collaborate on a latex document: take a look at some cloud LaTeX services such as Overleaf or ShareLatex.
3. Library Genesis (LibGen), SciHub: For downloading papers freely (kudos to Alexandra Elbakyan).
4. Mendeley: For reading PDFs, Mendeley is first recommendation, you can use it for multiple purposes: organizing/reading/highlighting… papers. If you just want a fast launching tool, try using SumatraPDF, a very light software. If you want to have more powerful tools such as commenting, adding signature… Foxit Reader is one of the best choices.
5. PDFsam: For merging/splitting PDFs
6. Notepad++, Sublime Text: For viewing/editing or even compiling codes etc.
7. Git, e.g. GitHub, Gitlab, and SourceForge: For collaborative documentation, research papers and source codes in addition to version control.
8. Endnote: It’s a reference manager and a MUST have. You can’t survive your Ph.D. without a reference manager.
9. Evernote: This app is superb in taking notes, setting reminders and many more things. Best friend of your overwhelming grad life.
10. Zotero: Available as a chrome extension. Really good tool for saving the websites you want to come back to.
11. MS word: I like to stick to the basic MS word and try not to make my life extra complicated. However, if your work involves math, latex is a great option.
12. Google drive: Must have. You never know what happens to these machines you have been saving your precious work on. Use cloud storage, Always.
13. Research gate: Your work simply doesn’t finish once it gets published. Share it on research gate. It’s like Facebook for researchers.
14. R and RStudio: R and RStudio is used for data analysis and creating graphs.
15. Markdown and Pandoc: It is used to plan text editor, write everything in Markdown, and then use Pandoc to convert writing into either an MS Word Doc or PDF Doc for submission. This fantastic alternative to writing in MS Word allows you to stop fiddling with formatting and focus on content.
16. Discovering Statistics Using xxx: You will have two versions of this statistics textbook, one for SPSS and one for R. It has most of what you need.
17. Google Scholar: Create alerts for terms and scholars in your area of specialization(s). And, of course, use advanced search features for finding publications (or entire literatures).
18. A word processor: Word is expensive. Google docs will suffice for most publications—and it’s better for collaboration. But there are other options.
19. Social media. Many scholars are active online. Some of publications and jobs are the product on online networking with scholars in your area(s). Twitter has been the most useful. LinkedIn is probably the second and Facebook is a distant third.
20. A portable computer. A laptop is essential for work, conferencing, presenting, analyzing data, traveling, writing, and all of the other tools above. Don’t get a tablet—they’re still just toys marketed as computers; they don’t do real work. Get something that will last the duration of your graduate training (4–6 years).
21. Data backups. You cannot afford to lose your data, your work, your notes, presentations, teaching materials, etc. Backup to at least one external hard-drive and at least one cloud service (e.g., BackBlaze)—three or four backup methods is even better in case one backup fails.
22. Grammarly. Grammarly is very important for spell and grammar checking. It’s a very efficient tool to improve the quality of your written work. Grammarly comes as desktop application, browser extension, online dashboard.
23. Pomodoro. Some people are great time managers and can concentrate for too long but as per experience when the work load increases and you will have to interact with few undergrads as well, it becomes very difficult to concentrate on the most important part which is your thesis. This tool is very helping to get maximum use of time by scheduling work and break times.