In some respects I think "Thy will be done" are the four scariest words in the English language. Saying it--and really meaning it--means that you are giving up control to God.
This year I have prayed for a former student's life even though I knew she was terminally ill and even though I knew that we shouldn't pray for life--not when death's reward is heaven. I have prayed for certain couples with the hopes that they might part ways because I thought they would be better off with different partners. I pray each day for the safety and good health of family members even though Jesus said that none of us should love our parents or our children more than we love Him.
At the end of prayers like these, though, I force myself to add "Thy will be done." Sometimes I have to repeat it to myself several times because I want so badly for things to go my way when they clearly are going to go in another direction or need to go in another direction.
Saying "Thy will be done; Thy kingdom come" is an admission that we mortals can't understand the divine. We pray with the best of intentions, but we can't understand God's will. We take a leap of faith each time we say "Thy will be done."