Link posts in chains/webs

I am working on a site that will require posts to be linked to each other starting from base ‘nodes’ and expanding in webs (so the base may have three responses, each of which may have three more etc.

I then want to link this data to a visual web (such as http://www.thejit.com) which can be automatically updated as posts are added. I don’t know much about JSON but this seems like the correct way to somehow link the two.

My question is, is there a way to intuitively link and tier multiple posts within wordpress so the JSON library populates correctly with no manual input? Making a post a sub-post of another using post ID’s would make sense (if this could be done from the post-writing screen) but then how to extend that into the JSON library automatically…

Frankly, the whole thing is frying my brain. Any suggestions would be most appreciated.