There is one big decision you need to make about how to carry your gear: whether to use a trailer or not.
Here is what we used:
Tubus Cargo rear racks.
2 Ortlieb Backroller Plus rear panniers per person
Jim used an Ortlieb handlebar bag.
Amy used a custom frame bag by Carousel Design Works.
We did not carry day packs on our backs. Amy strapped a day pack on top of the rear rack (and also our trash bag) using a basket net. It was convenient to have the day pack along to use when we walked to places.
Jim strapped a short sil-nylon stuff sack with the tent and his rain gear onto the top of his rack with the tent poles and stakes carried in a longer sil-nylon velcroed directly to the rack.
This configuration worked out just fine for us. Here are comments about our choices:
We had plenty of capacity with this configuration, even for the occasional stretches where we had to carry a lot of food or water. We understand that the BOB trailers handle very well, but we didn't believe that the extra weight is worth hauling - (13.5-17 pounds for the trailer + ~2 pounds for the drybag that sits on the trailer, versus about 4.5 pounds per bike for the rear racks and panniers we used). No matter how well a trailer handles, it is simply easier to ride uphill when you have less weight to move. It is also one less set of moving parts to fail. The trailer also potentially complicates transport to and from the route.
With the weight we carried, we both felt our bikes handled very well, even with the bulk of the load carried on rear instead of front panniers. (note that the fact that the bikes handled well even with all the weight in the rear may be due to the fact that the Sycip brothers designed the frame geometry for this configuration, whereas an off-the-shelf frame will have different fork angle and herefore different handling.) For people hauling 30-50 pounds of stuff, the trailer may be the best option - but we STRONGLY encourage people to consider hauling 20 pounds of stuff and sticking with the simplicity of a pannier system. The configuration we used will not provide enough capacity for people who are carrying "too much stuff"; if you have a lot more stuff than we had, and don't have a trailer, then you need to add front rack and panniers, which in itself adds another ~4 pounds to the load.
Tubus racks and Ortlieb panniers have reputations for being sturdy and reliable, and are the brands of choice (as far as I can tell) for people taking long tours in third world countries. We had no problems with them. Reading about several GDR racers who broke Old Man Mountain racks during the race makes me hesitant about that brand. They used to be made in the US, but are now outsourced to Asia (confirmed by Jim who talked to them directly) and I suspect their quality has deteriorated. Note that the Adventure Cycling catalog still says they are made in the US and sings their praises - but the reports from the GDR racers are enough testimonial for me to choose Tubus instead.
Jim's Ortlieb handlebar bag was (of course) waterproof and very convenient for carrying an iPod, energy bars, bird book and other things requiring easy access. On the downside, it weighs about 1.5 pounds, and doesn't carry much weight.
Amy's Carousel Frame bag was awesome (with one exception mentioned below). In it I carried a DromLite 6 liter bladder. When the bladder had >4 liters of water I could not zip it closed, but it still worked fine with the zipper open, even with a full 6 liters of water. I found it a great way to carry the water - low and centered on the bike, and a very light weight way to carry a lot of water. On most days I carried 1-3 liters of water, my binoculars, a windbreaker, sunglasses, a few bars, sunscreen. With >4 liters of water in the frame bag, I couldn't fit the other things in there. It was very easy to reach the things in the bag while riding the bike. The capacity of the bag will depend on the size of your triangle and your tubing diameter. Jeff Boatman did a terrific job of sewing a perfectly fitting bag based on the cardboard pattern I sent him, and it was delightful to do business with him. The downside of the bag is that the paint under the velcro attachment tabs is slightly etched - I'm sure that's not from the velcro itself, it's from the grit that got between the velcro and the frame and then was ground into the paint. I've got a two coat paint job - the base color, and a top clear coat with small sparkly flecks. The area under the velcro tabs has lost it's sparkle - it's not scratched through to the bone though.
Most mountain bikers we see, either in person or in pictures on their GDR blogs, are carrying day packs. Neither of us did so because we don't like the way they feel while riding. I'm a comfort fanatic, and I like to have unfettered breeze on my torso on hot days. Jim carried a water bottle in a cage, and I carried a bladder with a hose in my frame bag so we both had easy access to water.
Jim carried a day pack and 6 liter DromLite in his pannier and never used either one. We had them along assuming we would need to carry the water on our backs to give us enough load capacity during the long stretches without access to water and groceries. But we were always able to fit our stuff into the panniers. When we needed to carry a lot of fluid, Jim just put quart bottles of juice into his panniers.
Note that many of the GDR racers don't use panniers - they strap a stuff sack to the top of a rack and carry a day pack. We carried more stuff than the racers carry, because we like to be comfortable at all times, and because we needed the multi-day food carrying capacity offered by the panniers.
I (Amy) carried a day pack and a trash bag on top of the rear rack, secured with a basket net. I kept my rain gear in the day pack so I could pack it when it was wet and not get the stuff in my panniers wet. By carrying the trash on the outside we didn't risk making a mess of the dry stuff in our panniers. Also, the basket net provides an essentially unlimited ability to add any shape and size bag to the top, much more flexible than regular straps -- good when we had several bags of potato chips to haul :)
If you've got questions about any of this, please don't hesitate to post a comment and I'll try to respond quickly.