Vym can do both node links and multiple roots.  You need to add the modifiers mode toolbar to get the node links.  Vym generates decently consistent XML, so you can even translate to full-on semantic modeling -> RDF, etc. Along those lines, check out full-on dynamic graph tools like Magnus Jacobsson's d3-graphviz.  He has some demos that work at the speed of a mindmapping brainstorm session.  Whiteboards are great and all, and accessible, but why do double data entry? Keep your models. Reuse.

https://cdn.fosstodon.org/media_attachments/files/111/194/503/346/188/009/original/4cbb5f13d1fe1c18.png