South African Airways A340-600's also have windows in the toilets.
I personally like the idea. During long haul daytime flights, its nice to see a little daylight when the crew have closed all the window blinds in the cabin to enable people to sleep after lunch.
I remember an old episode of Airport where John, the Heathrow station Manager for Qantas was joking about the passengers who would insist on closing the blind before they would use the toilet whilst at 36000 feet