First of all, make sure that you record all necessary and appropriate information: author, title, publisher, place of publication, volume, span of pages, date. It's probably easiest to keep this basic information about each sources on individual 3x5 or 4x6 notecards. This way when you come to creating the "Works Cited" or "References" at the end of your paper, you can easily alphabetize your cards to create the list. Also keep a running list of page numbers as you take notes, so you can identify the exact location of each piece of noted information. Remember, you will have to refer to these sources accurately, sometimes using page numbers within your paper and, depending on the type of source, using page numbers as part of your list of sources at the end of the paper.
Many people recommend taking all your notes on notecards. The advantage of notecards is that if you write very specific notes, or only one idea on one side of the card, you can then spread them out on a table and rearrange them as you are structuring your paper. They're also small and neat and can help you stay organized.
Some people find notecards too small and frustrating to work with when taking notes, and use a notebook instead. They leave plenty of space between notes and only write on one side of the page. Later, they either cut up their notes and arrange them as they would the cards, or they color code their notes to help them arrange information for sections or paragraphs of their paper.
When you take notes, your job is not to write everything down, nor is it a good idea to give into the temptation of photocopying pages or articles.
Notetaking is the process of extracting only the information that answers your research question or supports your working thesis directly. Notes can be in one of three forms: summary, paraphrase, or direct quotation. (It's a good idea to come up with a system-- you might simply label each card or note "s" "p" or "q"--as a way of keeping track of the kind of notes you took from a source.) Also, a direct quotation reproduces the source's words and punctuation exactly, so you add quotation marks around the sentence(s) to show this. Remember it is essential to record the exact page numbers of the specific notes, since you will need them later for your documentation.
Work carefully to make sure you have recorded the source of your notes, and the basic information you will need when citing your source, to save yourself a great deal of time and frustration--otherwise you will have to make extra trips to the library when writing your final draft.
While doing your research you will be making connections and synthesizing what you are learning. Some people find it useful to make "idea cards" or notes in which they write out the ideas and perceptions they are developing about their topic.
It may have struck you that you just read a lot of "re" words: re-read, re-organize, re-group, re-shuffle, re-think. That's right; working with your notes essentially means going back and reviewing how this "new" information fits with your own thoughts about the topic or issue of the research.
Grouping your notes should enable you to outline the major sections and then the paragraph of your research paper.