I've been playing around a bit more in arena mode.
Battle axes reign supreme (steel and adamantine) for most situations. Unarmored, battle axes are deadly. Wearing iron armor, battle axes are still best - but shortswords start to have a better chance. Steel armor shortswords seem to be a teensy bit better, or at least equal - pulling off quite a few kills by simply bleeding the opponent from thrusting. Using all adamantine makes the shortswords pull ahead, winning almost every fight (funnily enough its almost always death by losing a bunch of fingers and ears and such, which are apparently not protected by gauntlets or helms).
So apparently shortswords are good against very heavy armor, but in most cases battleaxes are the best. Spears had a good showing for armored fights too, but they mostly just inflict red wounds and disable opponents and they wind up dieing to a bunch of pokes (one fight the spear guy managed to inflict red wounds to both the axe dwarf's eyes, then he bled to death). Spears would suck vs anything that doesn't bleed, though - so not very practical in fortress mode.
And hammers still suck against pretty much any situation unless made out of non-weapon materials (platinum is good), and even then they don't stand up to a good steel or adamantine battle axe.