I use a bungee to strap my locks to one side of my rack. Pannier goes on the other side. Flat kit in a small saddle bag, frame pump mounted on the frame (this sounds obvious but I see lots of people carrying them elsewhere).

Wallet, keys and cell phone all go in the pannier. If I'm without a pannier, I cram my ID, phone and $20 into my saddlebag with my flat kit.