Fact is, the controller is more appropriate, as the gaming device used as the program icon for an emulator is much more symbolic of a 'gaming' theme of the emulator. The logo of the console that looks like PJ64, the abbreviation of "Project64", at the same time just isn't as symbolic, but would make an excellent website banner. I mean, one, you don't use the console's logo as your emulator's icon, and, two, even when viewed as PJ64; the image of the controller actually gives a more graphical representation of Project64 as a gaming software than some 3-dimensional text....
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