Recogito, part of Pelagios Network, is an open-source annotation platform for places. The application is web-based and allows you to identify and record different places in historical texts, maps and tables.
Hypothes.is is an open-source annotation tool that allows you to enable sentence-level note-taking on web pages and files, including PDFs. It is collaborative, web-based, and can be integrated with different learning management systems like Canvas, which makes the tool particularly useful for classes.