Linux hands down is going to be more profitable if you know what you're doing.  We ran extensive tests on 58xx and 69xx systems running both Windows XP and Ubuntu 11 even with the "limited" overclocking controls we found Linux to be faster by far than Windows.  Keep in mind that we first searched for the sweet spot of profitability, sometimes overclocking reduces your profit margin.

Long term this is a game about maximizing profit, and while maxing out MH/s seems like the thing to do, you should be much more concerned with MH/J, we found that over clocking outside of the 'normal' settings, resulted in a lower MH/J in all cases.