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I'm a first year PhD student.
I'm in my first stage (doing a literature review) but I face problem in organizing the papers I read and the notes I take for all papers. Should I put all that in one MS Word file for example, or different MS word files, or maybe use a different software?
I don't want to come after month from now and get confused about the way I organize my papers and notes in.
So, any helpful ideas?
First of all, a graduate school is a learning process so finding what is perfect from you from the start is a valiant endeavour but not necessarily sure fire.
You should start to use a data base system, some (mentioned in comments) that come to mind are Mendeley (free), EndNote (commercial), RefBase (free) to mention a few. If you consider going into LateX (which many of us swear by) then I can recommend JabRef (free; BibTeX format). There is also a Wikipedia comparison page that can be of assistance.
To sort your references concerns managing some form of structure where you group or "mind map your articles. In the old days you simply kept them in piles. With a data base software you can start providing key words in the data base and also keep some short notes for each paper which makes everything searchable and ready for sorting. I think the process or sorting articles is one that changes with different tasks and also persons so you are best of taking some advice from others and looking into it. Hopefully you also have peers around who can provide their insights. In the end you will develop your own set of tools that suit your needs and to keep trying different ones at an early stage, and discarding many of them, is far better than trying to do it later when the mass of information is much larger. Another option is to simply start using something and sticking with it regardless of weaknesses.
The bottom line is that with experience you will rely less and less on note-taking and be more efficient at seeing structure in what you read and so keeping a reference database is the main tool you will use. Even if this may not sound very constructive, I also say that the time you spend now on testing different solutions will pay back later, putting it off is only pushing problems forward.
A final personal note. If you want a free, platform independent, and completely versatile way to author documents you should look into LaTeX-writing (for example through TeX.stackexchange). I recommend it to everyone unless you are in a complete Word-environment, being alone with a different system can be hard. You should nevertheless look into it.
I'm a first year myself, so I can't say "this works" so much as "this is what I'm trying"... But what I'm trying is using Zotero & Zotfile to hold notes on individual papers, and after reading each one I to try to fit it into a structure in a mind map (I use X-Mind).
I electronically highlight and comment my papers in the program Xournal. I used to then organize them somewhat in a program called Zotero (in some ways similar to the Mendeley mentioned above I believe). However, I recently stopped using Zotero because it was an additional hassle.
So currently I just mark up papers in Xournal and then organize them into different directories within my Dropbox account. I'm happy with this, and have been doing it for about 4 years now.
I used to use a journal to keep track of my readings as I could take the journal to the library with me. If I were doing a similar thing today, I'd use a wiki to keep track of my notes and research as that would let me re-organize things as needed, host PDFs of the journal articles when available and allow for searching.
