The Cornell Note-Taking Method
The Cornell note-taking method has been around for quite some time, first published in Walter Pauk's book How to Study in College, yet many people still swear by it. Gina Trapani wrote a nice introduction to it on Lifehacker.com. You can design and print your own custom note-taking paper if you want, or go with the original version.
Note-taking Software
Evernote is a free note-taking application that can be used via the Web or using a client for computer or mobile devices. You can use it to type notes, capture audio notes, and upload documents to your account; the company allows other software developers to work with it and as a result has many other software packages that will sync notes and documents with Evernote.
Evernote offers premium and business accounts which offer additional features, including the ability to save larger files and create presentations within Evernote.
Need some suggestions on how to organize your Evernote to improve your productivity? This article by Michael Hyatt shows you how to tag things more efficiently.
As part of the Office suite of tools, OneNote has a native Windows client, but also allows you to work online via a Live.com/Outlook.com account. If you have an iPad, iPhone, iPod touch, or Android device, there's also a free app that syncs with Microsoft's servers, allowing you access to your OneNote notebooks.