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Visual Understanding Environment
It is free software, with compiled Java binaries ready for download (somehow, not many people like to compile Java source code - neither do I).
I tried various mindmapping tools, but they didn't work quite as I would like. VUE works way better for how I want to use mindmapping.
You can draw arbitrary graphs, not only trees. You can label edges and even draw edges from an edge to another edge. Default rapid prototyping is optimised for drawing trees with a few extra internal edges.
It saves to reasonable XML. I invested some coding time into the problem; now it is sometimes faster for me to outline and export a few pages in VUE than to type them in Vim.
It has some nice tools and some nice shortcuts. I have yet a lot to learn here, but there are many tools that help me to sketch and navigate the mindmaps I draw.
Question: Does it allow you to generate new layouts with the same nodes? Being able to write a new node wherever I want, connect it to related nodes, and then let the program figure out how to place it all is one feature of yEd that I can't quite do without.
There might be other diagram program that let you do that, but I haven't found it yet. Granted, I haven't been looking long.
You can rearange nodes at will, you can select some nodes and ask VUE to rearrange them, you can select one node and ask to rearrange all the rest with this node as root of the rearrangement.
Note that VUE takes into account the order of edge creation when rearranging nodes; if you want it to change the order in which edges go out of some node, you may have to recreate these edges or use some other functionality for this that I haven't yet found