Comment Re:R language (Score 1) 180
I'd also suggest R. One of the problems with visualizing complex data sets is that, almost by definition, the prepackaged graphics tools don't allow you to create custom-designed graphics that suit the particular data-set you're working with. But with a bit of programming in R you can get amazing results.
There are some R packages that can help too -- I write about one of them, ggplot, here. (Disclaimer: I work for a company that provides support for R.)