The kidneys? If the kidney's stop working, they won't be able to get rid of excess fluid and this fluid will back up into your body, including your lungs.  This will make it hard to breathe.  Likewise, if the composition of electrolytes is out of whack because your body isn't exceting them, this can cause your body to not work right, and can effect your breathing.  This can happen when your kidneys fail (increase electrolytes) and also with excessive vomiting decreased electrolytes.  

In the end, all your body systems work together in a united fashion to maintain homeostasis (normalcy) in your body so everything continues to function in a normal fashion.  This is one of the reasons why in RT school we had to pretty much learn about all the body systems, and not just the lungs.  Great question.  You made me think.