Booze also fiddles with your immune system's cytokines, chemical messengers that can trigger acute inflammation–a.k.a. pain–in your noggin and elsewhere. (A small dose of an anti-inflammatory such as ibuprofen may help.)
If you were knocking back bourbon instead of, say, vodka, your head might be pounding a little harder. In general, darker hard liquors (and most beers and dark wines) contain more congeners, chemicals that may exacerbate hangovers. Smoking cigs also multiplies the misery.