If I mostly want to keep my own document repository (pdf, word, etc) with search ability over all included documents and, maybe, the ability to do notations, is this the right tool? If not, any suggestions?
Yes, this can be used as a document manager for those purposes, with selected plugins (which ones are based on preference; the list is not too long [1]). It now has the ability open and annotate PDFs, although for a long time it did not. There are additional notetaking plugins.
It doesn't have all the features of traditional document managers, but it will be far better for handling annotations.
I don't know much about JabRef itself, but a quick search seems to indicate that one of the key differences is word document integration - JabRef is focused on bibtex.
