Over the last few days, O'Reilly's Alex Howard (aka @digiphile) has published a series of very informative interviews with data journalists. As journalists get more and more sophisticated in collecting, collating, analyzing and visualizing data, their learnings are really useful for anyone working with data. The interviews contain lots of great insight, very useful information, and interesting links to more resources and examples, and I encourage you to read them in their entirety (see links below).
However, most interesting to me are the tools that the interviewees mention and which Alex calls the "Newsroom Stack". Any number of those tools may be used in sequence to get from your set of data to useful insights. I used the additional comments from the journalists to add to my own list of useful data tools; some key ones below, the rest on the Health Data Innovation Tools page. Let me know what other tools you think I should add.