My 3DS XL is Blue/Black, but the pen is just Black. I know you are asking for 3DS pen colours, but I also have DS Lite ones. One Pink, and the other Lime Green (they match the corresponding DS Lite colours).
Mine is green
My bird chewed up the thing that kept the original black stylus in place in the stylus slot, so i had to get a new one. (He chewed this one up too though so I have to shove it in weird to get it to stay ;v