I actually had this idea a couple years back and thought about developing something myself but I am pretty well convinced I'll never get to it. :) So I figured I just share it here and see if perhaps it makes sense for it to be considered for a Brickset feature.
The idea is pretty simple: you supply a list of sets you want (which could just be all of your wanted sets, but not necessarily - though this would be a good starting point) and the prices they go for at a given store. It then tells you which ones you should pair up for a BOGO (or BTGO as is sometimes the case) sale. Now, I realize this isn't really rockset science, however, there are a number of variables that can make it tricky. First off, if something is not in stock when you go to the store, it can really foul up your plans. The BOGO Helper, though, would just allow you to mark sets as excluded and reshuffle everything for you, giving you an updated optimal plan of attack. Additionally, it could allow ad-hoc price adjustments if, for example, it turns out that some set is on clearance at the store you happen to go into. Finally, an advanced feature could include the ability to optimize over multiple stores in the case of two different BOGO sales happening at once (such as durring the holidays).
I should add that, as far as maintaining inventories and pricing for a given store, this could be a community effort (wiki style, maybe), so as to make additional involvment on the part of the admin as low as possible.
Not only would this making planning Lego shopping trips a bit easier, it would also be a great way to show your significant other how much money you are about to save. :)
Let me know what you think.