Reference manager with note-taking/quote-storing capabilities
I use BibTeX / BibLaTeX with Jabref.
I make use of the Annotation Field.
See this TeX.SE answer for some details on how to enable the annotation tab on all entry types.

In JabRef, the search bar allows you to search all fields, so that gives you searching. I particularly like getting search results from my annotations and from the abstracts.
And you can store by each of the fields -- including the timestamp of when you added it.
It also lets you easily link to the PDF and/or URL/DOI. I suggest if you can link to the URL/DOI in preference, since that will work on any computer if you transfer the entry.

To add things to Jabref is just a matter of pasting the BibTeX entry code -- or it has a number of other options.

Jabref just fronts the BibTex file, which is really nice if you need Bibtex to use latex referencing -- but I guess for most fields of humanities this is not so significant.

BibTeX is also really nice because it is just plaintext field, so you can version control it cleanly.
See this Tex.SE question
Even if in humanities, version controlling your referencing is a great idea, since it makes it centrally available (if you use hosting), and gives you backup, and merging.