Allowing users to create multiple "notebooks" of nodes
We did the on a Drupal 6 site a few years ago.

If you want a single notebook, or have a fixed number of notebooks, then you can use Flags.

Our client wanted an unlimited number of notebooks, so we went the node references.

Basically, we created a "notebook" content type, with a few fields on it.  One of the fields held the noderefs of everything that was saved.  We may have also had some metadata for each saved item.  It's a mostly straightforward approach, but it involves a decent of plumbing to add/remove things (the unlimited number of notebooks complicates some scenarios), and you also need to consider all of the use cases you want with regards to how notebooks will be managed.

If we had to do this again with Drupal 7, then I would likely still go with nodes and entity references, potentially using field collections to bundle the entityref with metadata for a saved item.