Microsoft Excel became one of my best friends during my undergrad years. I could load in all of my data and with a few clicks have almost any calculation performed for me. I could also make important visual representations of my data. I still use Excel quite a lot to this day.
In my hunt for other programs to make organizing data easier, I found a site with a list of 22 helpful programs. These programs ranged from data cleaners, to various different types of data analyzers and visual applications. Some of these programs are paid, but there is usually a free edition of it as well. A few of the specific programs that I found interesting were The R Project, Google Fusion, and Many Eyes. Check out the website here http://www.computerworld.com/s/article/9215504/22_free_tools_for_data_visualization_and_analysis