To name a few: d3.js spring layout for web / d3 integration; Excel to Graphviz for ease of data prep; UMAP, tSNE, Graphistry, LGL for scale; Gephi for UI; Tom Sawyer and yWorks for breadth and pro support. NodeXL for analysis. WebCoLA for nesting/constraints.
Graphviz is such an underrated design tool. In every software project, someone is going to draw a graph of boxes with lines between them to describe the system and graphviz dot is still the easiest and fastest way to do that digitally.