A thorough write up

I remember being fascinated by a list of words I read in an English grammar text book. It was a list of words ending in -ough, and not one of them was pronounced the same way. Through, thorough, rough, cough, enough, dough, bough... I came across this list long after I was already fluent in English and could, in that mysterious way that first-language speakers can, use and pronounce all those words correctly already - so the list entertained me rather than depressing me. I recall feeling desperately sorry for an adult who was trying to learn English though. Or for teachers of second-language students: how would you explain those differences?

Recently I've been thinking that "-ough" has some company in the confusing-English-anomalies game. Consider the word "up", and how many different ways it can be used.
Grow up.
Shut up.
Hurry up.
Move up.
Keep up (different to upkeep, mind you)
Write up.
Round up.
Finish up.
Call up.
Saddle up.
Tie up.
Whip up.
Dream up.

Yup yup. I give up.