Some people might already know this, but after years of struggling ripping sprites or doing maps, I finally found a way to have the black background color changed to something else when removing the background layer in FCEUX.
Just open the fceux.cfg file with Notepad++, go to "gNoBGFillColor" and change the number to something else. I haven't found the number for pink yet, but I settled with "35", which gives me a purplish color that I don't think is used by any game.