A system, method, and apparatus for annotating an electronic document independently of its content is provided. According to one variation, a tablet and stylus-based computer is programmed with a document browser that permits a user to annotate documents viewed through the browser. The annotations are stored separately from the viewed document pages but are correlated with the pages such that when a previously annotated page is revisited, annotations relating to that page are retrieved and displayed on top of the page as an “ink” layer. Three different annotation modes are possible: ink, highlight, and erase. Each mode can be selected through a user interface supplied through the browser or through controls embedded in a document.