My rule of thumb is that if I'm using a coupon, groupon, etc, I'll tip on the full pre-discount amount. But if the restaurant is offering lower prices or specials, like during happy hour, then I'll tip on the actual bill.

I'll sometimes round up on drinks (not food) if the prices are really cheap, e.g., if it's dollar draft night, I will tip more than 15-20 cents per round.