Graphic design for dynamic weapon/armor on sprite
http://esotericsoftware.com/
This is an animation program specifically made for 2D sprite animation. It is very reasonably priced at $60. The easiest solution to your problem, and probably very close to what Maple Story does from the sound of ti.
Spriter is also a good tool for 2d animation. I'd suggest checking it out too.
">Here's a video about it too.
With a paperdoll system, the weapon and armor are on a separate layer than the character base. (So are hair, eyes, tattoos, anything customizable gets its own layer of spritesheet.) Each time the player changes equipment you programatically merge the layers into a single-layer spritesheet to display. ImageMagick is one such program that is used to do this. But yes, each weapon does need to have it's own animated sprite. If it's just an pivot animation (e.g. facing right and swinging a sword up and down) or a slide animation (e.g. facing right and poking a sword forward), that's quite simple, but sideways or diagonal attacks are more of an animation challenge.