Depending on the topic I'm working on, sometimes I need an approach similar to what you explained. I still use a mindmap, open a first-level node called 'temp' and start adding everything there and keep sorting them. As soon as a structure starts to emerge, I create other nodes and move those items to their new places. This is based on the assumption that your final output would be a tree with one-to-many relationships rather than a graph with many-to-many relationships. I've seen tools for organizing many-to-many relationships, but I never had the need to use one.