For Internet based research work (and play) I use a simple workflow. I use de.icio.us for saving a link with minimal personal context and Google Notes, when I am collecting information from different sources and adding notes and comments to them for further use (Blog or Work). Zotero, the free and open source  Firefox extension takes it to a sophisticated height.  Developed by Center for History and New Media at George Mason University Zotero helps you gather, organize, and analyze sources (citations, full texts, web pages, images, and other objects), and lets you share the results of your research in a variety of ways.

You can capture full web pages, PDF or images; categorize and tag them, take notes and make comments and search your source collection, all from the comfort zone of your browser. For heavy duty research work, a must try.

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