I'll usually tip on the pre-tax, pre-coupon amount. I do make an exception, though, for a few places (chains, mostly) which ALWAYS have certain discounts or which run them very regularly and where I don't go in without the discount. For those, I'll generally tip lower - if 20% of the pre-tax, after coupon amount is still an OK (10-15%) tip based on the pre-coupon amount, I'll usually leave that.

Example:
Local chain, pretty much always has "your second entree for $3.99" coupons
Two entrees, normall $13, $12 (and overpriced without hte coupon) and two drinks $2 each.
subtotal: $29, tip - 20% tip - $5.80
Subtotal with coupon: $21.01 - 20% tip - $4.20 - or 14.4%. Good enough for me.

On a flat out BOGO deal, that might end up being too low. Just sort of something to be aware of rather than hard and fast rules.