Record citation information (i.e. author, title, publisher, date, page numbers, etc) for your Works Cited or Bibliography page. A reference program such as Zotero can help you to organize this information and build a bibliography. Gathering this information as you research and take notes means that you don't have to find the resource again later.
Include page numbers in your notes. This will help later with citations or if you need to return to the source for clarification.
Organize your notes in a way that makes sense to you. Sometimes, it can be helpful to make a chart or draw a diagram.
Write down significant quotes and ideas. The point of note taking is not to rewrite the entire book or article. Instead, focus on making clear, succinct notes that will help you remember the basic idea of what the author is saying.
Paraphrase or put your notes in your own words.
Write down new or unfamiliar ideas. If the author doesn't fully explain an idea you may need to look for additional resources.
Interact with the material. Ask questions as you read. Does the author's argument support his or her thesis? Is the argument consistent? Does what the author is saying line up with what you already know about the subject?
Write legibly and use abbreviations that you will understand later. Part of the point of taking notes is to be able to review them later when you write your paper.