Among the basic aquarium medication mentioned here, two of the most common, which I normally use are Methylene Blue and Potassium Permanganate. Both chemicals are widely applied as antifungal remedy especially to treat some common fungus infection including mouth and fin rot disease. These two chemicals also do not leave harmful effects that could endanger the fish or human skin in contact, thus would be deemed safe and recommended for general usage. Usually a good practice when using aquarium medication is to remove all the aquarium plants and decoration before applying the solution.
Based on my own experience, it should be best that one should never ever use the chemicals as prolonged treatment. Depending on which type of medication, the correct usage should involve a short dip that lasts no longer than 8 hours period before doing a water change. This preventive measure is also important to ensure that the chemicals also do not harm beneficial bacteria residing in your tank and therefore, a short dip is enough when applying treatment. Chemicals such as Formalin, which are normally used to counter heavy infestation of Ich, also do not remain stable in water and the effectiveness will only last for about 2 hours. As such, there is no reason to leave the chemical much longer than the period suggested.
Another important thing, which you should always keep in mind, is that whenever handling aquarium medications, one should take precautionary measures to wear glove so that it will not stain the skin. Malachite Green especially those that contains zinc in the formulary, although will easily kill most parasites and bacteria can be hazardous when it comes into contact with the skin.