Depends on the pack!

I use the army type packs (Webtex bergan and now Snugpak Rocketpak) which have two large side pouches and main central bag.

I put the shelter, hygiene and stuff i wont use during the day in the central bit, lightest stuff at the bottom (so usually tent, sleeping bag, food and hygiene kit) and then day kit (clothing layers, that days food, water, brew kit etc) into the sides. In the top pouch I just put misc items...such as maps, torch, first aid... any overspill from the sides...

General rule of thumb is lightest at the bottom, heaviest at the top, day kit in easy to access areas.