I try to do like Turtle with the colored bag system, but I tend to pre-pack my meals in ziplocks... e.g., my breakfast is oatmeal, so i put a half cup of oatmeal, a tbsp of Nido powder, a tbsp of brown sugar, and a handful of raisins in a bag, roll it up, and that's a breakfast. I often tuck a teabag in with it, so i'm not looking for that elsewhere (i'm very uncoordinated when i wake up, and truly hate mornings.) My lunches look like MREs... a ziplock containing a bagel, jerky/landjaeger, tea, cocoa, or soup, cheese stick, and some dried fruit. Dinner is mostly Hawkvittles, so they're self contained. I'll take all my breakfast bags and put them in a plastic shopping bag of a color, and do the same with the lunches and dinners. My variation is a 4th bag which contains snacks, drink mixes, and (in a zip lock) some paper towels. I calculate about 3 sheets per day, mostly to wipe out my pot.
Other than meals, I don't use a lot of them for organizing anything... I rely on a simple one-big-compartment pack design for things like cookware, shelter, bedding, food bag, and clothes, inside a garbage bag if backpacking or drybag if canoeing. I prefer 3 outer compartments (two small one large) as carriers for water bottles and as a 'junk drawer' containing everything else. The junk drawer items that can't get wet go in a small orange dry bag. the others just go in the pocket. My hatchet tucks in with one water bottle, and a saw goes in the other if long, or in the junk drawer if short/folding. My cell phone goes in its own dry bag in my pocket. Spare batteries get taped together and dated for rotation, in the orange bag, along with my TP, First Aid Kit, repair kit, pad and paper, and headlamp. Things like sunscreen, bug spray, compass, bungies, cordage, spoon, sheath knife, water treatment, hygiene kit (toothbrush, paste, comb, soap, washcloth, pack towel) etc, don't care if they get wet, and go loose in the junk drawer. Sometimes the hygiene kit goes inside the pack.
I did just get a nice Sea To Summit drybag with integrated pack harness for Christmas, which has no outside pockets, but that's just for canoe trips, and I'll keep my water in a small pack that gets attached to it during portages. The rest of the system will stay pretty much the same.