See, that's the problem. I can't "accept" the idea of a human monk besting a dragon. (This is a failure of imagination, not a philosophical or realism stand.) Is it ironic or maybe part of the problem that I have empty-hand martial arts training (in real life)?
I have a mental stumble when imagining and describing a human monk killing an ogre; that stumble is a complete face-down fall when the monk is a halfling. I've stopped even trying to give the killing blow from the halfling a descriptive narrative. I now just say, "It falls dead."
I mean, the halfling comes up to the ogre's knee. I can imagine the halfling hurting an ogre, even stunning it, but it's the killing the ogre that's . . . killing me. How do you describe the killing blow on an ogre from a halfling monk?
It's not the halfling's strength (which is figured into the game mechanics), but it's the reach. Unless that punch to the ogre's shin travels up through the leg, through the abdomen, and up to the chest, I can't get my head around a halfling monk stopping an ogre's heart.
I guess I do need to embrace the idea that monk damage is pseudo "magical" and not actual physical. I think I can get that better. Sitting here thinking about it, I think I should go that route in my mental descriptions for the halfling monk.
Bullgrit
Well, I had empty-handed martial arts training before, and I have no problems with D&D monks killing dragons. I think it's more of your personal views... would I be correct that you don't see high level fighters as superhuman, but merely very well trained?
Anyway, I think you could just treat monks in D&D as having a specific type of physical magic. Mages bend reality with their invocations, Priests by channeling divine power, Psionicists use the untapped power of the mind, and Monks have learned to channel Ki to perform their own unique type of magic. Their abilities already reflect that, with them being able to treat their attacks as magical as they rise in level.
The issue of size and anatomy is an annoying one though, but there are usually options, especially for humanoids. The easiest is probably the heavy blow on the weakened enemy causes the enemy to pass out or even die from pain/shock. I suppose this helps further when you play with hit location systems and you have stuff KOed/killed from blows to areas that are usually not as vital.
Alternatively, take to the air! Spin kicks to the head, a leaping uppercut, or an aerial backfist to the back of the neck. However, if you want something more normal, treat the attack as a combination. Kick to the back of the knees or an attack on the groin lowers enemy for anything from a necksnap, strike to a nerve point behind the ear, etc.
That is more for humanoids and decent-sized creatures with a reasonable anatomy. Anything huge or unusual, well, you pretty much have to fall back to hit very hard, though there's always different ways to describe the attacks. This may be abhorrent to some, but you can take a look at some videos of fighting games like Street Fighter, Tekken and whatnot for ideas.