I don't really have a system. But, when I am cleaning my kitchen every evening, I sometimes look around for something I can swipe at with the paper towel before I toss it. The dust on the canisters or the back of the stove, behind the faucet, the window sill, and sometimes I swipe one of the shelves in the fridge, alternating of course.
So no real system other than just looking around and seeing what else I can swipe at before I toss the paper towel. Please, nobody tell me how much more economical it is to clean with cloths or microfiber cloths. I clean the rest of my house with those but the kitchen I use paper towels I can toss. Primarily because I don't want bits of food encrusted cloths lounging around in the laundry hamper in a house with cats :)
I don't do spring cleaning. Every week I have one day I look around and just do what looks like it needs done whether it is dusting, etc.