Organize weapons and armor by types, or characters. I don't have many weapons so that's easy for me, but the armor is a bit of a pain. I do bags of things like "high resist armor" and "LRC armor", if you have lots of LRC armor you might want to make a couple bags worth of meddable 8 piece 100% suits for any new characters you might want to train (or lend to a friend.)
I would make one bag for stackable items and secure it somewhere convenient, as you come across something that stacks just drop it on the chest and sort later. Scrolls and bottles would go with regs, bandies would go with arrows and bolts, leather and ingots and wood, etc.
Make chests for your rare/nice items, and chests for house deco stuff where you can keep placement tools and interior decorators as well. You can put quite a bit into these chests, so you might want to seperate by types of furniture, deeded items that are also furniture, deeded items that go on the walls could go in with paintings and tapestries.
Basically when I sort stuff I put bags all around me (not chests, it's easier to move over a bag). I open them all up and then drag stuff to the appropriate bag.
BTW some items now stack that didn't used to. Tribal berries, savage kin paint, newly dug up granite and sand (must be dug post the stacking patch), I'm sure there are lots of items I'm forgetting. So that's can be a really nice space saver.