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I think Evernote is pretty decent for this. I just use the web version, but because of the work I do, I have to read a ton of documents online and usually want to refer to them later. Evernote helps because I can use the web clipper to save whatever I am looking at and then tag it and even write some notes on it. Then later I can fire up the desktop application and go through my notes.

I believe the mobile versions allow for hand writing but I've never used them.

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Have you considered Zotero? (oss addon for Firefox)

I like Evernote as well. It's far from perfect, but the ability to clip random bits of text or entire web pages along with plain notes is very useful.

The Web Clipper is very, very useful. It's almost replaced bookmarking for me. Actually, it's better than normal bookmarking since you can clip the important text, add your own note, and sync the whole thing to all your devices. Evernote's not perfect, but they've got this down great.

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