Usually I start with just one average joe chest (or two) then once I progress I will as quickly as possible make an Alchemical Chest for all my gear. As soon as possible I make a dozen Alc Chests and use pipes to sort them all with one Wooden chest for input. I usually divide into Ore's/Underground Loot, Crystals/Gems/Powders, Redpower & Redstone, EE, Tools, IC2/Buildcraft, 'tother mods, Wood, Natural/Mob Drops, Other. Its probably not the best once you get quite a few items but It's what I've been using recently.