A paper in the journal Alchoholism: Clinical and Experiment Research by researchers at Brown University reveals that the colour of alchoholic drinks really does affect how bad you feel the next morning. Darker drinks (such as whisky) contain more chemical by-products than do lighter ones (such as vodka). However, how you feel (in terms of hangover) does not necessary correlate with performance loss the next day. So you may feel better drinking vodka but you would be just as incapable of driving or using heavy machines etc than if you drank whisky – though the latter may make you feel worse.

See http://www3.interscience.wiley.com/journal/123216970/abstract