This wants to be a series of examples of how to do annotations on a chart. The idea is to find a format that is suitable for various charts and allows to build tools.
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Andrew Mollica, d3-ring-note D3 plugin for placing circle and text annotation, and HTML Annotation
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Scatterplot with d3-annotate, by Chris Polis, example using d3-annotate
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Rickshaw has an annotation tool
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Benn Stancil has an annotation example for a line chart
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Adam Pearce has arc-arrows and swoopy drag
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Micah Stubbs has a nice VR chart based on swoopy drag
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Scott Logic evokes “line annotation” in a graph (different concept).
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Seven Features You’ll Want In Your Next Charting Tool shows how the NYT does annotations
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John Burn-Murdoch example with adding/removing and repositioning annotations