the ladder sorting is by win % as isaac said, and then by points for and against during the season if there is a tie. at the end of the season it goes on head to head, which is a system AFAIK that it unique to FIBA, and which more sports should use.
So....If Adelaide play Perth 4 times, and Perth win 3 odf those four, and they are tied on wins at the season end, then Perth finish ahead of Adelaide.
You cannot apply this system during the season, but at the end of the year, it makes sense - its a tie breaker.
I wish the AFL used head to head, it would be a vastly superior system than for and against percentage, especially considering that teams like St Kilda and Essendon play almost all their home ganmes on guaranteed perfect conditions.