I encountered the same problem, but now have a partial solution:
If you want to refresh the list entirely, delete the .db file located in "~/Library/Application Support/Dock/", followed by running killall Dock. This forces the Dock to refresh its list of widgets. Unfortunately, the list of apps in Launchpad will also be reset.
You can remove these individually via
sqlite3 ~/Library/Application\ Support/Dock/*.db "DELETE from apps WHERE title='APP_NAME';" && killall Dock
(from http://www.wikihow.com/Delete-Apps-from-Launchpad-in-Mac-Os-X-Lion, which adds:
Replace APP_NAME with the name of the unwanted app as it’s displayed in LaunchPad.
)
I wish I knew how to add widgets manually, but I really don't know much unix... If it's any help to those trying to find a better solution, the widgets are located in /Library/Widgets.
Update
In the end I just decided to use Launchpad Manager to delete apps. It also functions as a widget manager.
Best Answer
The database it uses (a simple sql database) is located in ~/Library/Application Support/Dock. That holds all your apps and their placement.
You could back up the file (or simply use TM) so that it can be restored at a later date.