I used to take my notes on a sheet of paper, then I used end note software for recording bibliographic data of my research sources. I want to take my notes digitally and relate them to the bibliographic metadata.
Do you know Mendeley? It might be useful
http://www.mendeley.com/
Possibly you can use Endnote. There is an option in Endnote where you can write and save your notes as well as the PDF of the article and track back very fast when needed.
It actually depends - do you have an online or offline workflow for your research? There are some good academic and non-academic bookmarking/note taking tools that can help you either ways.
Online Workflow
a. Google scholar - This is where I start my research process often. I will start searching by keywords and start with most cited references. Based on relevancy to my research area, I will then save them to my library for future reference. Also useful to find all the related work of the author.
b. Paperpile - You can add all your references that you come across online, and all will go to your google docs. You can even download to .bib or endnote format as you wish. It’s not free but definitely a tool worth trying out. Google docs integration really makes it easy, as I can have all my references list from different sources in one place.
c. Pocket - Okay, this is a generic bookmarking tool, but you can tag all your research paper articles with the specific tag for future reference. This helps me collect online articles really fast and find my all research tagged sources at one place.
d. Highly - This tool lets you highlight articles online. What’s best about this chrome plugin is that, all your article highlights come as a feed on your highly home page, with the source also listed. Rather than collecting whole articles, it lets you collect part of articles that will help your work. This is really helpful in annotating parts of articles that I could refer back in the future.
Offline Workflow
Okay, so you would have already heard of Mendeley, Zotero etc. Especially if you already know the research papers you want to refer in the future, you can use these desktop softwares to quickly add your references in one place. One good thing about these softwares is that, you can quickly download all references in a .bib or endnote xml format that you can quickly integrate with your writing software.
a. Mendeley - You can search by those recently read, recently added, authors who wrote etc.
b. Zotero - Cleaner interface, easy to export all your references in one click.
In both cases, you can add all research papers to your collection and export them on to MS Word or Typeset when you are ready to start writing.
Few more I have heard of but haven’t used though - Papers, EndNote
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