Re:
I have partially understood your query but I would like to recommend you for deleting apps from iTunes.
First off, if you decide a particular app no longer stay; simply click on its icon in your apps library in iTunes and hit the delete key from your keyword.
Now, when you hit the delete, you are prompted with the warning that if you delete the app from the iTunes, it will be deleted from your iPhone next time you get sync.
Now click on delete the app button and this will ask you for moving the app to Trash if you want. Click on Move to Trash and then empty Trash.