This is commonly used in combination with other medacations but on its own is also used to treat Fungus on eggs, Ich, Saprolegnia and some bacteria (although generally not for use in bacterial infections other than as a bath/dip/quarantine therapy).
It is also effective in treatment of some gill diseases, especially from injury such as ammonia burns, nitrite posining or fluke damage as it transports oxygen allowing for more gill efficiency as well an aintiseptic aid in the healing of tissue damage.
Methylene Blue can also treat some protozoa although only a mildly effective for this it is more effective when used in combination treatments.
Paraphrased and condensed discription.