yEd Graph Editor
I downloaded yEd Graph Editor yesterday and found it really interesting, though I don't have a use for it yet.
When I read the description on the FreeDownloadADay.com e-mail it seemed run of the mill and something that you'd plug into excel to make a graph from data. When I checked it out I found out that the graphs aren't visual representations of numeric data, but points of correspondences between two or nodes. Cool! You can make flow chart diagrams with it, but a lot of other stuff as well. I was particularly taken with how you can alter the view (as per the examples above) to reflect what you want. Very neat. Lots of other stuff as well, but I haven't explored it properly yet.
Runs under Java and is freeware to boot.