Ha ha! I found that out when playing around with Zelda: A Link to the Past... It's how I managed to make Link's hair yellow! XD (Actually, you make OoT Link by only swapping some "colors").
Basically, the tile viewer shows you a sort of a default palette, like a, um... heat sensor? Basically, the viewer cannot call the palette that you're viewing so you're stuck seeing black/green/blue/white or whatever (that would be the case, at least, when hacking GB/C and NES games).
Let me explain in pictures...
Let see, in game you see this guy:

but the tile viewer shows you this guy:

(NOTE: this was not taken from a tile viewer, but it gets the point across, I think). That's how you're seeing it without the sprite's normal colors.
If you don't want to mess around with any palette changers or anything and if the color you want to change to is already in the palette, you can just use to recolor the sprite... Like...
Let's say you wanna give the koopa green eyes and gloves, so you get the green that at his feet

. In the viewer, that green may look red, purple, green, whatever, so you'll have to remember where they are. Anyway, figure out what color is used there and draw it on top of its hands and stuff to get this:

. You didn't have to use any palette things.
