I figured out how to do this but it's kinda technical. For me, I wanted to delete all the old Parallels windows app links.
First, you're going to need an SQLite database editor. I suggest SQLite Database Browser from:
http://sourceforge.net/projects/sql..._200_b1_osx.zip/download?use_mirror=softlayer
The Database that has Launchpad items is located in:
~/Library/Application\ Support/Dock/
It is named something like XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX.db
You need to copy that database over to your documents folder and edit it from there like this:
cp XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX.db ~/Documents/XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX.db.bak
Then open it in the SQLite browser and execute a query that will delete the items you don't want from the items and apps tables.
Example for Parallels windows app links:
DELETE FROM `items` WHERE `rowid` IN (SELECT `item_id` FROM `apps` WHERE `bundleid` LIKE 'com.parallels.winapp%');
DELETE FROM `apps` WHERE `bundleid` LIKE 'com.parallels.winapp%';
After that is done, you save the file and copy it back to the folder it came from... making sure to back up the original.
cp XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX.db XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX.db.bak
mv ~/Documents/XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX.db XXXXXXXX-XXXX-XXXX-XXXX-XXXXXXXXXXXX.db
Then you need to open up terminal and do a killall Dock... or force the Dock process to quit from the Activity Monitor. Then those problem icons will be gone.

If you have any questions let me know.