I have just tried out Scapple to create some diagrams, and I have been very impressed, creating something that could be pasted into Scrivener quite quickly. It seems very easy to use, and a lot more powerful than the very first release I tried out a long time ago. The diagram I created would have taken many hours using a drawing program such as Corel Draw.
One issue I have is that I have two columns each containing a stack of notes, with connections from notes in the left column to notes in the right column. Where the connections are horizontal, it is perfect, and the arrows clearly visible going between the sides of the notes. But where a note low down in one stack is connected to a note high up in the other stack, the connections move to the top and bottom of the respective notes, where they are hidden by the adjacent notes in the stacks. If the arrows could be forced to come out of the sides of the notes, as they do when the connected notes are level with each other, it would be much clearer, and you could actually see the arrow heads.
The reason why I am arranging things this way is that I have two lists and I want a visual representation of the different arrangements in the two lists. If something was top of one list but moved down to tenth in the second list, that is important, but the connection is hard to see
Maybe there is a way to do this, but I have not managed to find it.