I have a site running on php that uses Node for a few development tasks. Currently, our team relies on puppet to install the node modules that we use for these development task
As far as I have seen, package.json deals with a single directory's dependencies (and a single instance of node_modules).
Your best bet is to split your applications into separate directories.
Barring that, you could just add all of the dependencies to a single package.json file. It will install into the node_modules folder and any app within that directory will have access to all of the installed modules.