OP- I have (or had, actually) a Dakine Lg Campus backpack. Loved it for the organizational features, but it was uncomfortable to ride with. Then went for a Banjo Brothers Large pack because I didn't want to mess with any rain covers. Waterproof and comfortable while riding, but is lacking in the organizational area.

I tried the milk crate solution, but my packs when full just won't fit. My Banjo is a little too large to comfortably strap straight to the rear rack... so I got inventive. I put a flat beverage rack on my rack to widen the surface area for the backpack to sit on.