node-webkit (at this time) has an application folder under under process.env.LOCALAPPPATH (for windows users anyway) which could be used.
Another option which is viable is to use an application directory in the exe directory of the program.
IE for node with process global.
var path = require('path');
var appDir = path.dirname( process.execPath ) + path.sep + 'data' + path.sep;
//might produce something like c:\\programs\\node-webkit\\data\\