Since node-webkit version 0.6.1, you may retrieve the dataPath from the App object. The WebSQL files will be stored within the databases
folder.
Wiki: https://github.com/rogerwang/node-webkit/wiki/App
Get the application's data path in user's directory.
Windows: %LOCALAPPDATA%/;
Linux: ~/.config/;
OSX: ~/Library/Application Support/ where is the field in the manifest.
Example:
require('nw.gui').App.dataPath;