Unix command-line tools like awk and grep. Set operation commands are essential too (http://www.catonmat.net/blog/set-operations-in-unix-shell/)
Ruby/Python/Perl for more complex massaging and wrangling
Excel (yes, really) for quick stats and graphs, great 1st step in understanding what you have
D3.js for visualization
I've used R in the past, but I found I was trying to squeeze data into R models. D3 is pretty hard to grasp initially (I'm very much still learning) but I'm finding that it's helping me think through how to visualize the data I have, rather than just forcing it into one of a few standard charts.