Naruto - Broken arm, all of his skin burned off, had one of his lungs ripped out, paralyzed by Sasuke and dangled in the water (pile-driven head-first into rocks in the anime), stabbed multiple times by chakra blades, poked by Neji's 64-palm strikes, kissed Sasuke, had the crap beat out of him by a girl, poisoned, had his penis insulted, shoulder popped. Not to mention all of the really gory things that happened to some of his clones, like the juubi smashing one that was still alive for a few more panels.
Sasuke - When the curse seal was added it hurt so bad he fainted, Orochimaru's genjutsu made him puke, broken arm, eye ripped from its socket (even though it was just an illusion), broken ribs, stabbed by six or seven swords, had his chest and neck blasted open, partially cooked by Deidara, partially amaterasu-burned, wing chopped off, kissed Naruto.