Tools to (privately) annotate/markup a website for maintenance
Solution 1:
I found a browser plugin called iCyte which lets me highlight items on a page and add a tag and comment for each one. A thumbnail screenshot is saved with highlights for each page, and when you click on a "Cyte" the web page is loaded with your items of interest highlighted in green. I think iCyte stands for "Internet Citation," and it seems to be geared toward tracking your citations when working on a research paper.
You can filter by a single tag at a time, print a list, export to MS Word (actually, RTF format) and Excel (CSV), and make both private and public annotations and comments. You can also invite other people to work on a project with you, even if it's a private project. You can also copy Cytes to other projects.