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First of all, they have some similar functions. Like both of them allow use to use multiple tags. Also, their users can copy and paste from original article to appear in comments about site. In addition, they both provide following service, which means users can follow each others to know others' updates. And, they provide users with some Apps.
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In summary, both of them are useful web tools. Diigo is better for managing websites and contents, and Scoop.it is wonderful with smart search. I think I will use both of them for their different conveniences.