Link to nodes in WYSIWYG Editor and Domain Access
See the LinkIt project.

Its flexible API should let you hook into the node listing logic it uses to inject SQL to group node listing by Domain. You should be able to make a plugin with it ... I see no existing solution off-hand (I've used LinkIt and DomainAccess, but not had users linking around sub-domains from the WYSIWYG. My domains were very separate from one another).