Whatever controversies he's been embroiled in over the years, at the end of the day you cannot deny that the man is a legend and one of Australia's finest ever batsmen.
There are just too many wonderful knocks to pick from - some have already been mentioned here, but I think his twin tons in his 100th Test, which made a mockery of Graeme Smith's declaration, deserve mention. Even in his twilight years, he was capable of grinding out a double ton.
Even his captaincy was somewhat underrated - his ODI record has always been stellar while even at Test level, he seemed to have a plan B. I suspect the main reason why he appeared overly defensive towards the end of his captaincy reign is because of the unreliable bowlers he was saddled with - Johnson in particular.
Nobody here has mentioned his fielding, which was absolutely brilliant in his prime - even at the end, it was very good.
With all that being said, I believe it was a good time for him to retire. He could never capture the magic of his prime and his unselfish decision allows us to blood someone in his place for the 2013 Ashes.