On my New 3DS, I use the stylus it came with. On my old 3DS, I either use my paint brush stylus (It's not a real paintbrush, it's a 3DS stylus) or my fingers if I can't find that.
I use a one that came with my preorder of hhd, there were 2 new 3ds styluss/ styluses whats the plural idk;; and a bigger one that was like a chunky pen - which I now use
i think mine are DS Lite, i got a pack of them cheap from Gamestop i think i paid one dollar for some kind of DS Lite accessories pack, and it included like five styluses (stylii?). sometimes though i just use my finger tip. for a while when all the stylii were lost, i used the cap from a highlighter marker, it just seemed to have the right angled size on the tip and was a tad flexible (although very clumsy to use).