Diigo.com - Free account allow for unlimited bookmarks but has limitations on some of its other features. The Firefox add-on is excellent.

diigo.com —  Diigo - Web Highlighter and Sticky Notes, Online Bookmarking and Annotation, Personal Learning Network. Add comments

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Sitemark.com - social bookmarking website with a nice layout. visually appealing. links can be put into folders, rated, and tagged.

sitemark.com —  Sitemark - Save, organize, share and discover your favorite websites Add comments

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StumbleUpon.com - Not for bookmark organization. Good discovery engine with an excellent add-on. Attractive site.

stumbleupon.c... —  StumbleUpon.com: Discover the Best of the Web Add comments

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SecondBrain.com - Social bookmarking site. Decent bookmarklet. Can organize websites into collections with an automatic screenshot.

secondbrain.com —  Secondbrain Add comments

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Gemsta.com - Great. Allows storing of links, videos, images, text, products, & more. Good bookmarklet; Toolbar not Firefox 4.0 compatible.

gemsta.com —  Gemsta - Find It. Save It. Share It. Gemsta It.

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