Echoing TouristMSN, everyone does it differently. I often do it differently on different days.
I general, I start out on paper and divide stuff into categories:
First aid and Bike maintenance
Navigation and Communication
Food, snacks and cooking
Tent, Sleeping Bag
Daily clothing, on and off bike
Cold, Wet weather clothes
Toilet kit
I lay everything out on a piece of plywood to make sure I have it all.
Then it goes into 4 panniers based on when it gets used;
Left front: First aid, Bike tool kit, Snacks, Cache Battery for phone.
Left Rear: Rain Gear, Maps, Some clothes
Right Front: Stuff for making camp, Air Mattress, Camp shoes Toilet kit
Right Rear: Cooking gear
Stuff on the left is stuff I might want during the day, I can access them when the bike is leaning against a building. Stuff on the Right is for making camp when panniers may even be off bike.
Sleeping Bag is in a waterproof stuff sack on top of rack. Tent is also on top, it doesn't matter if it gets wet.
Probably left some stuff out, but yo can get the idea.