A missing one I use is zotero. You can take a snapshot of the webpage and add notes and link related content.
For pdfs, you can use a zotfile addon where you can highlight, add notes, etc. using your favourite pdf veiwer and zotfile will then grab those highlights and notes and put them into the zotero entry for that file. You can then view these without having to open the pdf and search through them. This is particularly handy for when the pdf is large.
Of course the final advantage of zotero is that you can then easily cite things, which was its main purpose.