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Lets get it straight. Many chemical compounds can be used to stain cells. Staining leads to higher contrast of the image observed under light microscope. Some stains also colourize the cell structure differently, so as to help you identify cell structure.
Methylene blue is one of the component in Gram's stain and Wright's stain, it makes the nuclear more visible.
Other stains, such as H&E stain (Hematoxyin and Eosin, stain nuclear component and cytoplasmid protein) and PARS stain (stains glycogen, glycoprotein and proteoglycans) are also very useful to stain animal cell, especially Pituitary cells.
Here is a detailed list of various biological stains. It serves as a brief note for you.
http://en.wikipedia.org/wiki/Staining_%28biology%29