It really pees me off when people say 'oh you look ill' or similar. I think its really rude and would never say that to anybody, even if they did look rough. My neighbour said that to me yesterday, which really cheered me up.
If I am thinking it I don't always say it because it makes you think you must be ill if someone says it. Better to have a glass half full than half empty so try and cheer them up not put them down.
I would say 'you dont look well' as then they might go and get it sorted or find a problem they didnt know about. I would never say to someone you are so skinny as I find that no different to saying 'you are fat'