Knuckle:
To knuckle under is to submit, give way, admit defeat. Why should you
put your knuckles under anything in order to express submission? The
saying seems to go back to the late 17th century tavern habit of
knocking the underside of the table when beaten in an argument; they
put their knuckles under.
Another source at Expressions & Origins says that, "Although
the word knuckle now generally signifies the finger-joint, it used to
be applied to other joints such as the knee. To knuckle under therefore
meant to bend the knee in respect or submission."
The same source goes on with:
"To knuckle down (apply oneself
diligently) is, however, a reference to the knuckle of the hand. The
term is from marbles, where the knuckle has to be placed down on the
ground when playing. It is an important rule of the game that the
knuckle must be placed exactly at the spot where one's previous marble
ended up. From this sense of strict observance of a rule comes the
modern sense of earnest application.
Near the knuckle (almost
indecent) is more dificult. It may come from an old proverb expressing
approval - 'The nearer the bone the sweeter the flesh [meat]' - or from
the old school punishment of rapping the knuckles of a child with a
ruler. The most likely explanation is that when carving a joint of meat
one may get 'near the knuckle [bone]' and be unable to cut any further;
thus a remark that is near the knuckle is close to the limit (of
propriety). There is in fact an expression 'near the bone' that means
the same."