[gardarh]

From what I understand being drunk when going to sleep relaxes the muscles around your throat increasing your chance of apnea. The relaxed muscles around the throat means that the airway closes yielding a similar effect to choking (which is essentially what apnea is). The end result is that you choke periodically throughout the night meaning that the quality of your sleep is much inferior to what it could be; this is probably a large contributing factor to hangovers.

Edit: My source is a knowledgeable person on the subject, feel free to contradict or doubt the truthfulness of the answer - makes sense to me at least.