I honestly don't have many store apps on my phone. The ones I use are Michael's and Walgreens, because like
@Cherylndesigns said... they're the ones where I see the most reward. Seriously love the Walgreens rewards program... Clara and I save up the points from buying normal, every day stuff and then go on a make up/fun stuff spree every once in a while.
Food apps: I used to use Domino's occasionally but the last time I ordered from our store, they called back about an hour later to cancel our order because a brawl had broken out among the employees! I use the Subway app any time I need to get sandwiches for anyone besides myself. It's easier to just hand everyone my phone and have them customize their own order in the app than counting on me to remember everything!
The other store app I use a lot is Amazon... but not to order. I love the scanning feature in the app and will scan things while I'm in the store to read reviews before I make a purchase (or scan books at the library).