EDIT: I missed the part where you said you tried Evernote
Evermore. Http://evernote.com. I had a large number of bookmarks and was having two problems. First, I was having a hard time keeping them organized and longed for a way of grouping favorites together without having to save in multiple locations. Secondly, some of the bookmarked pages would be removed by their owner.
Evermore has an extension for Chrome which lets me clip articles to Evernote where I have a copy even if the author takes down the original page. I can also apply tags to make the article searchable. Lastly, it gives me a link to the article where I can see the original page.
I use it for bookmarking news articles, how-tos and of course Cool Tools.
I use Evernote for a lot more than bookmarks, but I think it will meet your needs.
Did I mention they have clients for Windows, OS X, Android and iOS. You can also access your notes from their website.
Philip