I received a Thirty-One Tote as a baby shower gift. It is the perfect size to fit behind the seat in front of the car-seat. I love that everything is contained (remember I'm Type A) and that I can remove the whole bag for re-packing, cleaning, or date night.
I organize the bag with the most used items (food, toys, wipes) on the top and the lesser used items (rain cover, hats) on the bottom. About once a week, I have to pull the whole bag out of the car and reorganize everything - it also helps me feel less like my car has been taken over by the little one.
Food. Since my little man is quite the eater, I always keep some snack in the car. I keep them near the top since a hungry kid is an emergency. The Munchie Mug Snack Cup is one of my favorite inventions. The soft fabric keeps the stuff from spilling, but lets a hand in. The big handle means Baby Peach can grab on to it even when I am carrying him or he is in the stroller. The Munchie Mug also comes with a separate lid so if it is in my bag, I can seal it up completely. Baby Peach has not quite got the hang of grabbing just a few Cheerios at a time - so it can be a real mess. (Nothing that shaking out the car seat can't fix.) I used to be really worried about Baby Peach choking while I was driving so I stuck to Puffs (a variety of brands available) and Mum-Mumms, which basically melt in his mouth. He has pretty much mastered eating, so I've added GoGoSqueeZ apple sauce pouches and Kashi Cereal Bars to the "car snack" rotation. I keep a plastic bag full of these snacks in the car bag. I also keep a standard Munchkin 8oz sippy cup in the car. Its not our favorite cup, but it works and I wouldn't cry if it got lost.
Diaper Change. The real downside of cloth diapering is traveling. I almost always resort to disposables when we are on a long trip, but even short trips can provide a challenge. My car bag always has a full back of disposable inserts for the clot diapers. This way if I forgot to pack an extra insert (we used Flips) or we go through more then expected I can stay with the cloth diapers. I also keep a few disposable diapers in the car, because sometimes the cover becomes soiled and I don't have another. I also find you can never have too many diaper wipes or too many hand wipes, so an extra package of each of those go in the bag as well.
Comfort Items. I have a collection of items I keep in the bag designed to make Baby Peach or myself more comfortable regardless of unanticipated weather changes. A small lap quilt, which I have used for sitting on, nursing, playing peek-a-boo and providing shade. A small first aid kit from Medibuddy. A Balboa Baby Shopping Cart and High Chair Cover, which we use so much I ended up buying a second one for our other car. I also have a plastic bag full of extras - socks, cloth drool bibs, onesies, pants and t-shirt for mom. A plastic bag full of seasonal items - winter hat, mittens, sun hat, sunglasses, sunscreen and any other item that I may need to sub in or out of my diaper bag. I also keep a rain cover for the stroller. (I used to keep this rain cover in the house, but then I never had it when I needed it - this way rain doesn't dampen our plans.)
Obviously the items will continue to change as Baby Peach gets older, but curtailing his mess to one bag sure makes my car seem somewhat organized.