I think I have fought just about everything by now in my 7 years of reefing. Here is my list of pests starting with the worst:
1. Absolute worst by a large margin is aptasia. My infestation numbered in the thousands after a very unsuccessful long term battle. I tried CBB, 20 x berghia, kalk paste, peppermint shrimp, and even the electrified poker thingie that I think Paul B made. I finally gave up and took all the rocks out of my tank and moved them to a 32g trash can where I have been slowly starving the aptasia to death by denying them food and light. I think they have been in the trash can for 6 or 7 months now, and 99% of them have died. I realize that a quicker solution would have been to just completely kill my live rocks and start over, but they have 5-6 years of biodiversity built up on them by now, and I didn't want to lose that. I hope to have these completely beat within the next month or two.
2. AEFW. If you are lucky enough to catch them early, you *might* save half your corals. This is a very labor intensive battle because of all the dipping you have to do it insure they are all dead due to the fact that the dip doesn't kill the egg sack.
3. Dinoflagelates. People sometimes confuse cyano with dino's, but once you've had them you know that they aren't even close. Dinos are litterally a poison. Killed off all my snails and hermit crabs that had to walk through it, as well as my prized helfrici firefish that ate it and died a sad death. I finally kicked this one by doing a number of things including increasing my flow, opening up my rock work and massive amounts of water changes and wet skimming. I think it took 3-4 months.
4. Cirolanid Isopods. I was lucky to catch these while I was still curing my live rock, so they didn't make it to my new display. Took 6 months of setting "traps" and starving them out before I was finally rid of them and able to put my LR in my display.
5. Rock crab. My first batch of live rock came from Tampa bay saltwater, and among the many hitch hikers was a "cute little crab" that turned in to a vicious killer. By the time I figured out what was going on he had eaten 4 or 5 porcelain crabs, half a dozen snails and hermit crabs, and even an entire serpent star fish. This may seem like an easy fix, but man was it strong, and it was always able to get to a hole in a rock and hide. One day I finally thought I had killed the bastard when I ripped off his claw and stabbed him multiple times. Thinking I had won the battle, I replaced my clean up crew, and he went unseen for about 2 months. I again notice that my cleaning crew is gone, so I hatch a plan to stake out the tank late at night. Sure enough, the rock crab from hell emerges, and he is literally 3 times the size as when I had last seen him. I was so angry I chucked him off my balcony...
6. Bryopsis. Psh childs play =P Get some snails and boost up that mag. Seriously though I know this one is tough for some, but it went away easily for me.
The biggest thing though is just to never give up.
Peace,
Jesse