I have recently described a workflow for saving and annotating web pages as HTML files on the forum of Zotero (a tool for source management, for which this question is very relevant):
I have used a ‘what you see is what you get’ (WYSIWYG) editor, which
Wikipedia describes as “a system in which editing software allows
content to be edited in a form that resembles its appearance when
printed or displayed as a finished product”. Such an editor can be
used to highlight text of interest, and to add notes directly in the
text as well. For me, BlueGriffon (http://bluegriffon.org/) works.
One can add extra value by saving the edited file as a separate
version. Highlights and notes can then be extracted by computationally
checking differences compared to the original.
A very recent improvement of the answer:
After some more searching and testing, I found that the Firefox
annotation add-on TextMarker allows for easier highlighting than
BlueGriffon. Conveniently, highlighted regions can then be found (and
potentially extracted) in the HTML code by searching for
"textmarker-highlight".
TextMarker cannot remove highlights from local files, however, and
saving notes in local files looks quite messy. So it is probably best
to use it in combination with a WYSIWYG editor.