MediaGoblin, can host a little bit of everything and seems to have
come back to life as a project
Freeplane
Multiple root nodes
can be simulated with floating nodes: double [Ctrl]-click on the document
to add one.
This node is still attached to the root node. Create a child node, then
Format -> Edge Properties -> Styles -> Bezier on that child
node to get visible connections between child nodes in the floating
node back.