In a commercial scenario, a serious contestant for sure is yFiles for HTML:
It offers:
- Easy import of custom data (this interactive online demo seems to pretty much do exactly what the OP was looking for)
- Interactive editing for creating and manipulating the diagrams through user gestures (see the complete editor)
- A huge programming API for customizing each and every aspect of the library
- Support for grouping and nesting (both interactive, as well as through the layout algorithms)
- Does not depend on a specfic UI toolkit but supports integration into almost any existing Javascript toolkit (see the "integration" demos)
- Automatic layout (various styles, like "hierarchic", "organic", "orthogonal", "tree", "circular", "radial", and more)
- Automatic sophisticated edge routing (orthogonal and organic edge routing with obstacle avoidance)
- Incremental and partial layout (adding and removing elements and only slightly or not at all changing the rest of the diagram)
- Support for grouping and nesting (both interactive, as well as through the layout algorithms)
- Implementations of graph analysis algorithms (paths, centralities, network flows, etc.)
- Uses HTML 5 technologies like SVG+CSS and Canvas and modern Javascript leveraging properties and other more ES5 and ES6 features (but for the same reason will not run in IE versions 8 and lower).
- Uses a modular API that can be loaded on-demand using UMD loaders
Here is a sample rendering that shows most of the requested features:
Full disclosure: I work for yWorks, but on Stackoverflow I do not represent my employer.
