Evernote has very good PDF support but you need a premium subscription to make it actually useful. I clip PDFs to Evernote and annotate them all the time.
I've been thinking about this a bit today[1], because I fear that Evernote is dying. I love and pay for Evernote, but they've been stagnant for years now. They're slowly adding features, but absolutely nothing that I care about.
As far as I can tell, there's really no functional equivalent to what Evernote does: a bucket you can throw data into and search for it later. OneNote probably comes closest from a purely note-taking standpoint, but it's missing some of the key features. This makes me a little nervous, as I now realize how reliant I am on a tool that I have very little confidence in.
It does basic note taking and checklists and things pretty well (better than Evernote in some ways), but a frequent use case is creating a notebook with stuff in it (a mix of clipped web pages, notes, maybe documents), and then sharing it with someone. Also, it needs to be searchable. It's that part that OneNote seems weaker at.
As far as I can tell, there's really no functional equivalent to what Evernote does: a bucket you can throw data into and search for it later. OneNote probably comes closest from a purely note-taking standpoint, but it's missing some of the key features. This makes me a little nervous, as I now realize how reliant I am on a tool that I have very little confidence in.
[1] https://twitter.com/larrywright/status/643495960480509952