You can try Flamory. We build this tool to help people track their research without too much hassle. It automatically organizes the bookmarks you make into topics and shows a screenshot thumbnail for each of them.
You don't even have to bookmark every interesting article you find, because Flamory will save a couple of pages before and after your bookmark.
You can check out Flamory, it saves selection, position on the page and a screenshot - all at the same time.
Personally, I stopped tagging my bookmarks long time ago, because this tool can search by the whole content of bookmarked page. Every word from a page is now a tag :)
It works only on windows, though, as it integrates with the desktop applications.
When I read pdf books on my PC, I use flamory a lot. Basically, you can create bookmarks with this tool, and it will save a screenshot, selected text and exact location in the document. I can later draw some highlights over this screenshot or write notes as a text. But, usually having a screenshot is enough to remind me of my thoughts about that part.
The nice thing is that it collects bookmarks from multiple books and articles in one place, so I can search them all at the same time.
Too bad it works only on Windows, would be nice to have it on an iPad too.
Evernote works great if you move your whole life into it. But if you just want to organize the work you do in different applications, you can try Flamory. It creates smart bookmarks that work not only in browser, but also with the local files and Outlook emails. You can later find them using thumbnails, or by any word from the document you bookmarked.
You can share what you saved using the tools you like - just paste stuff into emails, wikis and other documents, even to Evernote and OneNote.
OneNote is great if you write a lot of notes yourself. But, if you mostly collect and then share stuff, Flamory will be way more efficient. I like that it does not force you to use it's own service and you can paste stuff from it to emails and wikis.
Why don't you keep the bookmarks outside the browser in some app that will store them locally on your disk? Evernote or OneNote can make page snapshots. They like to sync all your stuff to the cloud, though. You can also try Flamory, it keeps things on your pc only, and shows a thumbnail for every bookmark.