I had a serious mushroom problem a couple of years ago... the shrooms where going out of control and eventually started killing my SPS/ LPS colonies. I tried several different methods to get them under control and eventually found the ultimate solution to the mushroom problem: Reef Napalm.
Reef Napalm is an aptasia control method that I learned from Arcoholic. In a nutshell, it is a lye solution with an ultra high Ph and will basically kill any encrusting/ rapidly spreading coral that you want gone. Here is a detailed description:
http://www.atlantareefclub.org/forums/showthread.php?t=36190&highlight=aiptasia+treatment">http://www.atlantareefclub.org/forums/showthread.php?t=36190&highlight=aiptasia+treatment</a>
When I killed off the mushrooms, I made a batch of the Reef Napalm and used a syringe to administer the "medicine". I pushed the end of the syringe into the mouth of the mushroom and would administer the RN directly into its inner cavity. A few minutes later the mushrooms would literally disintegrate.
Mushrooms are incredibly resilient, so you may want to administer 2-3 doses to ensure that none of the remaining tissue cannot grow back into a colony. I would wait 24 hours in between treatments, but I was able to pretty much kill everything by the 3rd dose.
Prior to the napalm, I tried everything. This is the best mushroom killing method that I have ever used!
