For a while, I used a small Sea to Summit dry bag that was then clipped to the rear rails on my saddle. It was out of the way, but quite accessible, and kept my tools dry, which oddly, I find to be a priority because, while I might not use them often on a tour, I want them functioning when I do, not all covered in rust and non-functioning. Some of that philosophy has come from randonneuring, where you keep riding even when it's raining!

Other times, I've put it in the rear or side pocket of the pannier I am using at the time. That was I know where the tool bag is. More lately, I have used a ziploc bag which is lighter, almost as effective with water protection, but a little more flimsy.