Quite a while ago, I imported all my Delicious bookmarks into Evernote. I loved having all my information in one place, and did not want my bookmarks to be in a different place.
I gave up two things when I imported my bookmarks: Delicious' social aspects and Delicious' ability to warn that I'd already saved that URL.
I'm sure my Evernote now has many duplicate URL's captured in it.
I'd been hoping someone would write an app that would scan my Evernote database and identify duplicate URL's, or that I'd find the time and talent to create one. I'm still waiting.
Evernote themselves has made things a bit easier going forward. Their latest Web Clipper for Chrome shows you all the times you've captured URL's from the site you are currently on. At least if take a moment to review those before committing to the Clip, I can avoid adding duplicates in the future.
Unfortunately, if you haven't imported your Delicious bookmarks into Evernote, you cannot now. Last November I wrote about doing it, only to find out that Evernote had removed the Delicious import ability from their Settings page. They promised it would be back quickly, but seven months later, it still is not.
If you use Chrome, get the latest Web Clipper. If you are not using Chrome exclusively, why not? It is a great browser.