Data Visualization

• Paraview is a general purpose 3D visualization tool designed to handle extremely large datasets.  Visuals can be created interactively or via Paraview's scripting/batch processing (useful for large datasets where interaction becomes too slow).  Supports isosurfaces, cutting planes, streamlines, glyphs, volume rendering, clipping, height maps, and more.
• VisIt is another general purpose scientific visualization tool.  It supports 80 visualization techniques (contours, mesh, slices, volumes, molecules, etc) and can read over 110 different file formats. 
• VMD (Visual Molecular Dynamics) is an open-source molecular visualization program for displaying, animating, and analyzing large biomolecular systems.

Text Analysis

• Voyant - a web-based tool designed to facilitate reading and interpretive practices for digital humanist students and scholars.  Can create a variety of visualizations based on text data including word clouds, bubblelines, textual arcs, word trees, stream graphs, scatterplots, and more.

Graphs & Networks

• Gephi - open source software that can handle 50K nodes and over a million edges.  Gephi can handle and animate dynamic networks (networks that change over time) and outperforms other tools when working with large networks.
• Cytoscape - open source project aimed more supporting biology applications than Gephi, also can create graphs and network diagrams with large numbers of nodes and edges.  Cytoscape also can work with more input formats and features plugins that add additional functionality.
• Tulip - is another open source network visualization tool with the most self-explanatory interface of the three tools listed here.  Another notable feature of tulip is that it supports edge-bundling (grouping of edges together). 

Timelines

• Timeline JS - creates a simple web timeline from a google sheet that incorporates pictures, descriptions in addition to a horizontal timeline. 
• TimeMapper - is an extension of Timeline JS that also include a map where events are located with markers.

Colour

• ColorBrewer - is a great resource for creating palettes of colours for use on a map or other visualization.  Also can provide advice on choosing palettes that work well for colourblind people, that are printer friendly, and that are photocopy safe.
• Colorgorical - is a more advanced tool that incorporates measures such as perceptual distance.  It also allows you to start with a colour (or several) and then assigns additional colours to the palette automatically based on the selected options.
• I Want Hue - another online tool for creating colour palettes with a colourblind safe setting.

Programming

• Processing is a programming environment designed for artists, designers, and others who have never created code before.  Good tutorials and support for creating interactive visuals.
• P5.js builds on Processing (and can use Processing code) but it operates within a web browser rather than as a stand-alone application.

APIs

• Google Charts - Charting library provided for free by google with wide variety of chart types (29+) with output in HTML5 and SVG.  Lacks some of the customization/animation/interaction elements supported by other libraries. 
• HighCharts - popular charting library with support for interactive visualizations.  More powerful than google charts, easier to use than D3.  Free for personal and academic use.
• D3 - steep learning curve but very powerful library for creating interactive and animated visualizations.  Very widely used, has a gallery with huge variety of examples to start from.

Approximately 80% or more of any visualization project is taken up in working with your data.  These are a few tools that may help in this process.

• Data Wrangler / Trifacta - Data wrangler is a Stanford/Berkeley Research project that makes it easy to interactively clean and transform your data.  It can handle 1000 rows for data, for bigger datasets work with a subset of the data on the wrangler website to setup the processing and then use wrangler to export a script file that will process your entire dataset.  Trifacta is the commercial continuation of this project that is free  for datasets < 100 MB.
• OpenRefine - is an open-source, free tool for cleaning up messy data.  It excels at normalizing data (e.g., imagine manually entered country names where the USA is spelled and/or abbreviated in 10s if not 100s of different ways - open refine can quickly fix these problems).  
• Tabula - extracts data-tables from PDF files into easy to work with text file or spreadsheet.