The unpleasant physical aftereffects from the use of alcohol (commonly called hangover) derive from excessive consumption of ethanol. Once the chemical reaches the stomach, about 20% of it make it straight to the bloodstream (the remaining 80% are absorbed by the small intestine). Once in the circulatory system, about 10% of the ethanol is eliminated by sweat, urine or exhaled through the lungs, while the remaining 90% build up in our toxin-processing plant, the liver, and primarily affect the Central Nervous System (CNS), causing the sensation of being drunk.
Inside the liver, hepatocyte cells produce enzymes that degrade ethanol into acetaldehyde, an even more poisonous substance that affects the oesophagus, liver, stomach, intestines and brain linings, causing gastritis, nausea, diarrhea and heartburn. In normal conditions (i.e. small quantities), acetaldehyde is converted into relatively harmless acetic acid by another enzyme, and drained from the liver to the bladder for imminent elimination. When acetaldehyde builds up within the body because of excess consumption, hangovers are likely to appear within hours.
This goes for the general principle, but things can get worse depending on what you have been drinking. Brown alcohols (rum, gold tequila, whiskey, etc.) contain a large quantity (as much as 2% by volume) of methanol, a substance that takes 10 times longer than ethanol to break down. If you can choose, go for clearer spirits, like vodka, which contain the least methanol.
One of the main impacts of alcohol byproducts on the organism is dehydratation. Alcohol is a diuretic, meaning that it prevents the kidneys from saving dihydrogen oxide from urine. The result is an excess loss of water, in quantities greater than those taken while drinking alcohol. The deficit of water is compensated by the body borrowing from stockpiled water in organs such as the brain. The loss of water in the brain causes it to shrink slightly, and because the brain's dura (the cortex enveloppe) is connected to the skull by pain-sensitive filaments, the deformation is likely to cause hangover-related headaches.
To make matters even worse, alcohol alters the flow of electrolyte ions through brain cells, slowing down the inter-neuronal transmission rate. Also, the liver glycogen reserve tends to deplete as alcohol breaks it down to glucose, which goes straight to the bladder for elimination (the glucose deficit is primarily responsible for shakiness, diziness, excessive sweating, blurred vision and tiredness).
You probably didn't know all this, notably that your brain shrank after binge drinking. Neither did I, and that's why I woke up with a bad headache at 04:00 pm today.
And I'm glad it was only vodka, methanol-wise.
Reference: http://www.gi.alaska.edu/ScienceForum/ASF14/1420.html