Diigo lets you annotate web pages and store them in a library in the cloud. It has a handy outliner feature to help you to organise your material and share the result. Its free account sets limits on how much you can store but paying a modest annual fee buys much higher limits. Teachers can get a free account with even higher limits.
It's worth investigating other programmes that let you grab web pages and annotate them. Evernote and Microsoft's OneNote both let you do this and mingle the annotated web pages with other media. They are particularly useful if you use mobile devices: the mobile versions of these apps let you connect to your library and download your notes wherever you can get an internet connection. If the web page that you grabbed is changed by its owner your copy is unaffected and your annotations remain intact. Each clipping you make is dated which is an advantage when it comes to creating a citation for that page if you quote from it.
Your module site may offer a Revision Notes facility. This allows you to make notes on the material by typing into a text box on the web page. Provided you click on the Save button your notes will appear next time you open the page.
Diigo can mark up both web pages and PDFs that are open in your browser. The techniques for PDFs are explained in the next section.