Yes, they do. From my experience, it is better that you let the cashier apply the coupon before swiping the debit/credit card, or else they end up calling the manager to do some type of manual override.
I have the Trader Joe's brand food worked out for WW points. I had posted it on that "other" site a while ago. If anyone would like me to post it here, just give me a shout. :)