A tip o’ the hat to /. for bringing this to our attention. Seems Hammad Siddiqi has published a scholarly scientific analysis of game theory applied to the question of whether to leave the toilet seat up or down. Here, in the introduction, he makes reference to two previous papers on the subject:

Both papers agree that the social norm of leaving the toilet seat down in inefficient in the sense that it does not minimize the total cost of toilet seat operations per household. However, both papers fail to address an important concern: If a female finds the toilet seat in a wrong position then she will most probably yell at the male involved. This yelling inflicts a cost on the male. Based on this omission, women may argue that the analysis in these papers is suspect.
In this paper, we internalize the cost of yelling and model the conflict as a non-cooperative game between two species, males and females.We find that the social norm of leaving the toilet seat down is inefficient. However, to our dismay, we also find that the social norm of always leaving the toilet seat down after use is not only a Nash equilibrium in pure strategies but is also trembling-hand perfect. So, we can complain all we like, but this norm is not likely to go away.
The Science Creative Quarterly » THE SOCIAL NORM OF LEAVING THE TOILET SEAT DOWN: A GAME THEORETIC ANALYSIS

A complete aside, but Pawn has for years maintained the authoritative assay on toilet tissue wrappers on the web. Check it out.