You might be looking for the Tabs Outliner Extension for Chrome. I've been using it heavily for the "middle-state" of saved and not open, but not bookmarked; now I'm looking for a "meta Tabs Outliner"-esque program, but I can't quite articulate my needs...
> What I want is to maintain a list of current references, preferably with some spatial context (tree-mode browsing is great for this) to what the relationship is between pages in my browser session.
Tabs Outliner puts every tab as a leaf in a tree, and you can nest leaves and affect the visual ordering on the tab bar at the same time - you can also do this reordering while the tab isn't even open! This is good for a while, but for me when I have thousands, it's lacking in some retrieval sense: I guess I want to query for just these tabs that have connections, and cross-reference research annotations on these sets of connections.
https://chrome.google.com/webstore/detail/tabs-outliner/eggk...