This is something I wrack my brain over constantly. There's got to be a better way.
In my home-built canoes, I can run paddles across the two thwarts situated on either side of the central third of the canoe length. This sucks when the bugs are bad, and doesn't offer much padding. If I want a dedicated yoke I can just build one and screw it into blocks glued to the gunwales; that works, but then you've got a bulky extra thing to tuck away or forget or lose somewhere.
Plastic boats are a different animal. I bought a clamp-on yoke for my OT Pack but it so clutzy and clunky that I returned it.
I bought a Dagger Solo 13 last summer with an interesting feature- a webbing strap that rolls up and tucks away on one side, with a corresponding buckle on the other; out of the way paddling, easy to click on when portaging, impossible to lose. There's a huge flaw in the design, though, in that the weight of the cane on your shoulders is enough to bend the gunwales in and create enough slack that you're bopping your head on the hull every step.
So in my next boat, I'm going to build on that concept and add a webbing strap with a buckle, just like the Dagger, but thread a thin quartersawn plank that runs maybe an inch less than the width between gunwales. This will tuck out of the way along the hull with a buckle, velcro, or snap when paddling, but shift the weight of the canoe onto the gunwales themselves during portage, rather than the mid-point between them, and reduce that tendency to sag inwards and reduce the distance between strap and hull.