I use mesh ditty bags and dry-bags for organizing while packing, since the goal is always weight reduction. Packing cubes work best in a suitcase, and so the benefits are lost in a backpack (you won't just be taking the cube out to put in in a dresser drawer)
I have a red drybag for my first aid, orange for survival/odds ends. thermal layers are kept in a sealine MAC bag (or whatever the surplus vented bags are called) sleeping gear goes in a sea-to-summit event compression bag. Food goes in dry-bags, along with stove kit. Fewer dry-bags and more mesh when its a dry walk (just pack liner) and more dry-bags for wet, paddle or similar trips. Since I often walk as a guide, I NEED bomber gear, so I end up a little on the heavy side. For the average guy, you can get away with a lot less. and its often easier to find multiple colors and sizes of simpler bags, without breaking the bank.
The advantage with drybags and mesh-string top bags is color coding is pretty easy. You can also do straight nylon string close bags as a lighter option. Its easy to add several pounds to your kit in bomb-proof drybags, but you often don't need them, depending on how you pack your gear, and other conditions. Where I work we use a system of color coded draw-string bags for stuff like kitchen kit, spare ropes and repair, and toilet gear.
