I chose cancer as so many people I've known have suffered from it.
In close second was Alzheimer's. Both of my parents have it right now, and it is appalling to watch their personalities, memories and sense of self vanish slowly as their brains die. I wouldn't wish it on my worst enemy.
It's a hard choice, because none is more deserving of a cure than any other. My family has been touched several times by cancer (with only one survivor to date), and that survivor (my grandmother) is now suffering from Alzheimers disease. It's a terrible thing to have happen to a loved one, and not be able to do anything about it.
I'm having a hard enough time dealing with cancer in the family - my aunt just got diagnosed with breast cancer and my mother just found a lump she's having tested - I couldn't imagine losing a family member but not really. That's how I see alzheimers. Losing someone without them going anywhere.