Currently, I am working to support ESL writers as they research for their dissertations, so I am always looking for tools that help them stay organized over months of reading and writing!

<--- That's my face as I search the web, high and lo, for free online tools.
I really enjoyed showing my students Weava the last couple years. Weava is a digital annotation software that has an extension that works directly with internet browsers, like Google Chrome, to highlight text/.PDFs. It stores the digital highlights and notes that are made in the user's account for future access.
I usually spend twenty minutes in class demoing and having students sign up for Weava. I assign a homework task that requires digital annotations to be submitted after the demo.
Even when I hear students probably won't use this tool, I like that the demo brings their attention to how efficient using software makes the research process. I especially love the color-coding highlight feature and that it stores the annotations online for easy access.
I am attaching my explanatory .PPT slides with screenshots to this post. I sometimes show students these slides, but I mostly use them to refresh myself on the features before demo day, and then I project my computer screen so the students can actually follow along with me on Weava.
Good luck! Happy annotating!