I tried phonegap and tideSDK and I concluded that node-webkit is much better for what I want (I don't like to build the app for each platform and also I can't build a windows desktop app if I am on linux etc.). I also liked the solution of meteor as a desktop app (as crazy as it sounds!). It provides mongodb out-of-the-box which is much easier to handle and it is much nicer solution from the other 3 solutions I have mentioned in my previous article.
I also watched a nice presentation for atom-shell and I am going to try it as well. Here is the atom-shell repository. My main issue so far was the backup/import and restore of the database. I finally tried websql for that, but it isn't ideal as you can't see the table structure if a table is empty, so I couldn't create a custom import/export functionality. I may try indexedDB, which I'll have to create a custom import/export functionality.