If apartments all had evenly sized rooms and uniform layouts, no roommates would ever feel jilted. For those living in rental reality, SplitTheRent.org offers a really precise web calculator to divvy up who should pay what each month.
[Update: Apologies for the duplicate post, but, hey, it is a pretty nifty calculator.]
You have to try it to believe it, although the explanations offered by Harvard astrophysics grad student Jonathan Bittner in the FAQ and How it Works sections show it's definitely more than a divide-by-X tool. Room sizes, window "awesomeness," closets, layout awkwardness, bathroom usage, and other factors are selected and factored in. At the end, you get your monthly rent sliced up for everybody. Now it's just a matter of getting everybody to pay their mathematical fair share.