I normally put different items in different containers.
Chest for weapons, Wardrobe for armors, Drawers for clothes, one small cupboard for Potions and one for Keys, larger cupboard for Books (as the Bookcases are annoying) then Barrels for Ingredients, Smithing and Enchanting materials, and one more for random things I've picked up during my travels like Bugs in Jars etc.
I've always used a system like H4RDC0R3V1B3Z described, used it in oblivion too. Though I've noticed my chest of random things is rather unruly, partly due to filled soul gems not stacking properly...
I think it would be great if someone made a mod that let you drill down a bit more finely. For example, if you have a chest of weapons, but you just want to look at bows, it can be a bit unruly. If you could just select weapons and then select bows, it would be much easier. Or maybe I should just sell more stuff/stop picking it up... --- "A man is nothing but his mind; if that be out of order, all's amiss, and if that be well, the rest is at ease." - Girolamo Cardano