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I've used org-noter to annotate PDFs in line, so I'd expect org-roam + links wouldn't hurt. Org will display images inline. I don't have a great answer for links into Excel. Do you need the data to "come back out", or just reference capability?

I can confirm org-roam links + org-noter works well for linking ideas between PDFs. I haven't found anything better, and regularly demo this to friends.

Related video demo: https://www.youtube.com/watch?v=Wy9WvF5gWYg

This is very interesting, will check it out. I really just need a reference capability.

Org export to CSV/TSV

Emacs pdf-tools mode is very much underrated. Checkout the list of org-roam ecosystem emacs packages. I don't know if Emacs supports excel or word.

I recently starte using MediaWiki as a personal kB. It works well with image, not sure about word/excel.

Definitely a richer ecosystem though.