Hacker News Reader

Mendeley or Zotero's tagging might work well for this. Both are more commonly used for organizing bibliographies in science, but should work here as well.

I store PDFs in Google Drive by quarter (e.g. ~/content/2015Q4/), and generally try to add a few relevant terms in the title. The only thing that bothers me is that I have to go through and specifically mark the files as available offline.

That actually sounds like a really good idea. Right now the only thing I for this is keeping a folder on my desktop titled "Reading Queue", and I drop symlinks in there to docs that I want to read sooner than later.