it was the saddest thing I ever saw!! He married Dr Corday, they had a baby (Ella). He developed a brain tumor that was eventually inoperable. He took his daughter Rachel on a tour of his life which ended with him teaching her to surf in Hawaii. He died in Hawaii while his family was on the beach. He never woke up
In the last scenes they showed as him walking through the halls of the empty ER.
It was season 8. The episode is called "on the beach"
OMG I cried!! I'm tearing up just remembering it. I always cry when a little girl loses her father.
edit....
I found the video of it
http://www.youtube.com/watch?v=LEiiIVwsFb8