A frequently held alternate interpretation
of the statement is that it means do what you have willed, i.e. do not give in to your weakness
This statement has a counterpart statement, and that statement is "Love is the Law, love under Will". "Do what thou wilt shall be the whole of the law" usually starts texts written by Thelemites, and "Love is the Law, love under Will" finishes them. It is incorrect to state one without the other, as the Book of the Law is a book that contains the creeds of two different Gods and preaches balance between the two, and the two statements sum up their creeds.
Crowley got the idea for this phrase from Francis Rabelais, who stated in Chapter 1 of Gargantua and Pantagruel "Do what thou wilt". (thanks keops)