Antiprotozoans and Antihelminthics (dewormors)
Medications to treat against protozoans and worms when used as a bath are not safe for invertebrates. This includes reef tanks with corals. All of the things here are very bad for corals and should not be used (with the exception of praziquantel which you still shouldn't use in your reef without desperate circumstances)
Copper used to be a great medication for most protozoans and worms however there is now a resistance of some Cryptocaryon and most Brooklynella and Amyloodinium as well as the flatworm Neobenedinia to it. Using it as a prophylactic in quarantine especially for Cryptocaryon is still a good idea
Treating fish for 12 days with copper (cupramine is safe and easy to test) in a quarantine aquarium will ensure no Cryptocaryon remain on the fish and no new parasites have attached.
Leaving a reef tank fallow (no fish) for 3+ months is the best way to eradicate the parasite from a reef system.
Running copper for 3 months is best way in fish only system.
Keep copper levels above 0.2 parts per million (0.3 parts per million is best bet)
Ideally test using the hach copper meter (egg). The chemetrics low range comparator vacuum ampules are also very accurate and easy to use but expensive. The salifert test kit can help in a pinch but is not very accurate...don't bother with the seachem copper test in my experience.
Formalin is a poison. it kill anything at a high enough concentration (it's used to preserve tissue). If you get the concentration right you can kill most protozoans and not the fish. It degrades in the environment pretty quickly and so multiple treatments are necessary. This stuff is carcinogenic and so using proper protection is important.
Formalin is still very effective at treating Amyloodinium with pretty good success by administering 1 ml per 10 gal (38 liters) every other day for 14 days in a qt system and watching fish for signs of disease. The parasite will have fully fallen off and subsequent swimming stages will die from the continued presence of drug in the water.
For fish already with Amyloodinium, a treatment in an out of tank container (a dip) of 2 ml in 10 gal of water will actually cause most/all of the parasites to fall off after 2 hours. The parasites which fell off can still be ineffective if formalin levels go down so clean out the treatment receptacle after use and dry out thoroughly
Formalin is difficult to find for hobbyists but there are approved versions of it for aquaculture which a veterinarian can prescribe. Mardel still had a product out called "Quick Cure" which is formalin and malachite green and can be dosed as described here. Seachem has a prodcut called paraguard which is very similar to formalin and supposedly as effective.
This antimalarian drug is a cousin of quinine which we find in tonic water. It is safe, easily dissolved, and effective again most protozoans to an extent. It is most commonly used recently to control Brooklynella hostilis is fish only and quarantine aquariums.
It is measurable by a tool called a spectrophotometer which costs thousands of dollars but because the drug is relatively safe, a decent scale is all you need to administer this medication reasonably. The half-life in salt water is about a week and the drug is effective at around 10 mg/liter (38 mg/gal) and not dangerous until much higher and so a weekly dose of 20 mg/l works well to control most strains of Brooklynella.
A dewormor specific to flatworm parasites (platihelmenthes) common in the aquarium trade, this drug can be toxic at just 4x the therapeutic dose causing blindness and other neurological symptoms in fish and sharks and so accurately measuring and dispensing this is critical. It also does not mix well with water and so strategies for getting into the system involve putting it directly into the inflow of a large pump, dissolving it with vodka at a rate of 1.5 ml vodka per gram prazi (might get small bacterial bloom from carbon dosing). prazi also has the unfortunate eventual circumstance of being eaten by certain types of bacteria. As you use it in a system long term (months) a bacterial population grows and makes the need for higher doses and more frequent treatments necessary to control flatworms in old tanks. In quarantine and 1 run treatment regimes though you wont find this situation. The external flatworm Neobenedenia mellini is the most common parasite people see in their aquariums for which this is the best treatment option.
Prazi is treated at 4mg/liter every 10 days for 3 treatments to break the life cycle of flatworms. This kills adults then kills babies as they emerge from eggs days/weeks later before they can grow up and reproduce.
Prazquantel is safer in medicated food as it seems that the gut selectively uptakes what it needs rather than the gills absorbing it indiscriminately. Feed has proven to help with external flatworms though total eradication of a high parasite burden in a system is unlikely by this method.
A prepackaged version of praziquantel is called Prazipro but for anything larger than 100 gallon tank this can get very expensive vs buying over the counter more bulk versions of the drug. the main advantage is that in Prazipro, the drug is already evenly dissolved.
A few people seem to be allergic to this and get a rash when in contact with it so use proper protection.