Doing research, there are plenty of stuff we should take care of, different articles and notes, websites etc..
It is sometimes hard to stay ordered and not to get lost in too many pieces of information. How do you organize your work? Are there any helpful software tools to conduct research projects — in my case, a thesis?
For me, it is difficult to give a fit-for-all answer. The best method is the method that you are most comfortable with. Different people use different tools. My M.Sc. thesis supervisor was a believer in taking notes in paper notebooks. I prefer to construct a set of structured folders in my PC and and use them for managing different aspects of a project (codes, texts, papers, notes, media, etc.). Of course, there are software tools that can be helpful too. As Elad Den has answered, reference tools are very helpful (I have personally used Zotero but couldn't like it much and ultimately used plain BibTex files).
On the other hand, there are project management tools that some people are very comfortable with (after all, a thesis is a big project). Trello is a popular and free tool that is very simple to use (I have used it for non-research projects and was very comfortable with it and I believe that it has potentials for managing research projects). Evernote is also another tool that is great for taking notes and has some project management features.
Generally, and based on my personal observations, it mostly depends on your personal preferences and I believe that it is a good investment to spend some time on trying different methods and finding (and/or fine-tuning) your approach. Also, it is not a bad idea to have a talk with your supervisor and have his/her opinion.
I recommend working with reference tools such as the likes of Jabref (or Mendeley or Refworks or whatnot). They are bibliography tools, but they can also be used to orginise your references. You can add the abstracts and your own notes. The great advantage in using such tools is that when the day comes to use this information in your thesis your bibliographical database will be ready.
Outlook is good for organizing meetings, seminars and other events in calendar. Onenote is quite good as well, although I don't know if it is has project management features as MxNx said Evernote has. You can also consider online repositories as a way to inspire progress. Research-gate for example is not just a repository, but a way to update projects. Outlook is also the ideal way to manage your various mail accounts. You can add more than one email and also group categories, such as supervisory team, writing groups etc. You can even make a team in outlook, which allows you to send emails to select groups of people in one click.
Others have also mentioned tools such as Mendeley, personally I use Endnote to organize my references and annotated bibliographies. I don't upload my papers, so I didn't see the need to branch out into Mendeley. Instead I use separate folders for each task. You can use Mindmappers to conceptually organize your ideas. You an also use a tool such as Harzing's Publish or Perish to keep track of citations by researcher and other parameters, or simply use alerts in Google Scholar etc.
