I really love Scapple for organizing research. Putting together ideas, files and concepts on a limitless space in a non-hierarchical manner is really great. Scapple is by far one of the best mind-mapping tools that I have tested so far. However, to make it even more powerful I would have some suggestions.
add scaleable background images, for example horizontal and vertical lines (with adjustable distance). I use Scapple for time-lines and it would be cool to use background lines as indicator for days, years etc.
Add a comment or note feature. As I said, I use Scapple for research and sometimes need to write memos for certain nodes (for example when Data is incomplete or whether I need to check an idea). Memos would be cool to keep track of things that need to be done
It would be helpful to give names to the connecting lines and arrows, which would enhance usability for flow-charts or causal chains
Also, add the MacOSX quick-look feature for documents that are embedded within the mindmap. Other mind mapping tools do this and it is great
Make a mobile version (iPad) to edit on the go
Ok, thanks!