DIRECTIONS:
Here is how I do it. Bear Hunter from this forum helped me out. I think this method is better than setting up transparent icons for apps or using steffwiz's blank apps. If you tap on those they both launch programs, steffwiz launches safari and the transparent icon would launch whatever app you have set as transparent. This will appear to launch something, but it will exit immediately, much cleaner in my opinion in case you accidentally tap on one of them.
First, download the blank.app.zip file I have attached to this post. Extract it.
Then, SSH into your phone and navigate to the / folder and then go into the Applications folder.
Upload the Blank.app folder that you extracted from the zip file and chmod the folder recursively to 755.
Now reboot/respring your iPhone and the Blank dummy app should be there. You won't be able to see it, but if you place your finger on the next empty spot next to your last icon on your home screen it should cause your other icons to wiggle.
If you want more than one Blank.app do not just copy Blank.app to the Applications folder again. Read the DIRECTIONS.png that is included in the zip. You have to change the lines shown in bold and you have to rename the Blank.app folder accordingly before uploading; Blank2.app, Blank3.app, etc etc.
TROUBLESHOOTING (if you can't find the blank icon on the screen):
When I first installed these I couldn't get the blank dummy icons to show up no matter what I tried. The problem was Boss Prefs, make sure they are not set to hidden in Boss Prefs Poof functionality. If they are set to ON and they still aren't showing up then try to reinstall Boss Prefs and they should show up. I recently restored my iPhone and when I reinstalled my dummy apps they weren't showing up even though they weren't set to hidden in Boss Prefs, so I reinstalled Boss Prefs and they magically showed up. Might work for you too, if you did all of the other steps correctly.