Bezier curve handles for links
When using the Expanded View, it would be very helpful to be able to control the flow of the links between thoughts to route them around other thoughts that might cross their path because the network is too dense or perhaps just to keep things tidy. This could be done with the use of bezier handles which are used in countless other applications. You could allow the user to insert one or more handles into a link, represented by tiny squares or something. Then, the link would pass through all the handles on its path to where the user wants it to go.
This is only useful for Expanded View, of course, and the handles should be a property of the view rather than the link, similar to the position of the thought on the screen relative to other thoughts when we use Expanded View.