Most ppl have stated on the boards that by mid-late game, money is NOT a problem. Therefore added expence for SBs will probably not cause any limiting in the number of SB in the empire. I can see the point in frogboy's suggestion. With that in mind, another thought line would be to only allow SBs in sectors that you control a planet in, or one that has an open resource in it (controlling a resource would have the same effect as controlling a planet in that sector). You would not have to have the majority of influence there, just and established presence (or open resource).
If you wanted to culture bomb a sector, you would have to capture one of the systems (or one next door) by traditional warfare first. And yes, I agree the culture "bug" is a valid point, but again, I feel the point of this thread was to see what might be the best way to limit the number of SBs. When I am rolling in several hundred B per turn, have spending at 100%, I could care less what a SB costs.
If cost is to be the controlling factor in building SBs, I still think my previous thought is a good one

. If it is going to cost me 100B more a turn for my 20th SB, then I might reconsider it. Maybe not.
Limit by upkeep cost (either by per module,or multiply maint for each additional). and/or
Limit by required sector presence. and/or
Limit by population or total # planets controlled.
I think there should be a decision on which way this fish is going to flop. Once that is decided, then actual numbers/costs/ect can be fine tuned.