How can I annotate a web article? More generally, what "workflow" do people suggest when dealing with web articles in research?

I used to always save useful articles as PDFs to my Documents folder, and maybe copy and paste useful information I found to a word processor document. I have realized this is inefficient for a number of reasons, and found simply bookmarking useful articles and organizing those bookmarks in a nested file system (in Safari) to be a more elegant, clean work process.
Is there any similar minimalist process for annotating those web articles? I know Evernote and others have a web annotator, but I'm hesitant to deal with external software... a feature integrated into Safari would be ideal.

Can anyone recommend how they deal with web articles when researching?
You may want to try Microsoft OneNote. When you copy content from a website and paste it into a notebook, OneNote automatically appends the website URL. You can thus collect all relevant snippets without losing track of where they came from, and add your thoughts there.