Though oft-touted as being a good "cure-all" for bacterial as well as protozoan pestilences of aquarium life, Methylene Blue is best described as a decent baceriostatic, safe chemical to help reduce the presence, spread of bacterial and fungal complaints on freshwater fish eggs... Best actually used as a simple dip additive, by itself or in conjunction with other compounds... to reduce the amount of light as well as aid in oxygen carrying capacity (often important).
A tri-cyclic compound: 3,7-bis(dimethlamino)-phenazathionium chloride
Methylene Blue, Methylthionate Chloride, Urolene Blue. A stock solution (3.7 mg/ml.) can be made by dissolving 1.4 grams of powder in 380 ml.s of water. In actual practice, most folks simply buy stock solutions.
Most promisingly as a preventative... against fungal and bacterial action on freshwater fish eggs. Though sometimes suggested as a treatment for ich, velvet, Cryptocaryon, Amyloodinium, other protozoa, monogenetic trematodes... there are far more useful medicines for actual treatment of these pathogens.
Toxic to aquarium plant life, as well as nitrifying bacteria... Methylene Blue should not be used for prolonged exposure, or in permanent (main, display) systems... as it can/will kill off necessary beneficial bacteria.
There is evidence that utilizing Methylene Blue in concentration in the process of acclimating marine livestock reduces toxicity of nitrite and cyanide. The author (RMF) has used Methylene Blue as such a dip/bath adjunct for many years with good success. Please see here re: Dips/Baths. Methylene Blue converts otherwise bound Methemoglobin back to useful Hemoglobin in fishes' blood... it is useful in the in situ detoxification of nitrite and cyanide... Useful in dips/baths of newly imported livestock indeed.
Other than the contraindications stated above (not to be placed in long term contact, not with live plants)... Methylene Blue is relatively non-toxic in a very wide range of concentrations. Often, aquarists are advised to "just place as much as turns the water very blue"...
Use With Other Chemicals:
Methylene Blue can be safely mixed, added with other dip/bath compounds... it has no synergistic or antagonistic property with any known chemical used for aquarium medicine.
Though you may find folks advocating Methylene Blue as a "first line" treatment for bacterial, protozoan, even metazoan aquarium life treatment (even here!), you are advised that there are far more efficacious medicines for these groups of pathogens. This being stated, there is no harm in having Methylene Blue as an addition... or using it where it is best... as a dip/bath additive or in fungal prevention in freshwater fish culture. Be aware that this materi medica is phytotoxic, will stain most everything in prolonged contact, concentration... and can kill off your nitrifying (biofilter) bacteria. It should NOT be placed in continuous presence (in main/display) tanks for these reasons, and is not useful as a net/specimen container disinfectant.
Andrews, Chris, Exell, Adrian and Neville Carrington. 1988. The Manual of Fish Health. Tetra Press, NJ. 208 pp.
Herwig, Nelson. 1979. Handbook of Drugs and Chemicals Used in the Treatment of Fish Diseases. Charles Thomas, Illinois. 272 pp.
Noga, Edward. 1996. Fish Disease. Diagnosis and Treatment. Mosby-Year Book, Missouri. 367 pp.