Well, traditionally the item found in the dungeon is used to kill the monster, so it seems like that should at least occasionally factor in. Seems like we need a kit for making bosses and several parameters. Parameters like, I dunno,
Health, fatigue, weakpoints, behavior, maneuvers, armor, lair and minions. Fatigue amounts to that stun thing you were talking about. It'd be a threshold for damage done a certain way to stun a monster. Like a secondary weak-point that I have to cause 3 points of fatigue to to stun it and gain access to the primary weakpoint to cause damage. For instance, shooting Queen Gohma in the eye so she's stunned and you can slice at her with your sword.
Behavior would list what it does, perhaps under what circumstances (just guidelines, perhaps an intelligence threshold for how often it will break from predictibility, 1 being never, some higher number being highly adaptive to the heroes), maneuvers would be how it attacks (a list of attacks it would use, along with if they expose any weakpoints and such, and perhaps warning signs a perceptive player can see and predict it is going to do. For lulz, some bosses have a few different moves with the same warning), a lair is what environmental hazards and such are in the place you fight it, minions are, well, minions. Armor would really be pointless, if it's entire purpose is to curtail normal damage. The only use I can think of for it is a boss has a set amount that's too much for a low level character, but they could come back to it later and be powerful enough to defeat it with normal attacks, just to show how far the party has come. Otherwise, I'd just say that most bosses, unless it's for something interesting, should simply negate the damage from normal strikes.