I save money by swapping cards in and out of my EDH decks rather than owning many duplicates. It's a very tiring task that I'm moving away from by just downgrading some of my decks; however, I still need to do it on some cards (Sylvan Library). I wrote a bookmarklet to help with the bookkeeping by generating an index of shared cards across the decks.

The script does the following:
(1) Retrieves all of your visible decks (i.e. ones that aren't minimized in folders). Note that this script will hit deckbox once per visible deck, so please don't go overboard with it.
(2) Determines which cards are used more times than you own in your inventory.
(3) Prints out one list per deck of all the shared cards in each deck. It also prints out a unique list of shared cards across all visible decks. See the attached screenshot for the output.

I'm putting this here in case anybody else is looking for something similar.

To install the bookmarklet, do the following:
(1) Bookmark any page and put the bookmark in your bookmarks bar.
(2) Edit the bookmark.
(3) Rename it something memorable like "Deckbox Shared"
(4) Copy the code from the link below and paste it into the URL field of the bookmark:
https://raw.githubusercontent.com/webercoder/deckbox-shared-cards/master/bookmarklet-deckbox-shared-cards.min.js
(5) Save the bookmark.
(6) Click the bookmark while on Deckbox.

The source code is here, feel free to submit PRs if you'd like:
https://github.com/webercoder/deckbox-shared-cards

I've only used it in Chrome so please let me know if you have trouble with it in other browsers.