If you didn't organize it as such initially it might be a huge ordeal, but I just named one of my retainers armoury and keep all weapons, armor, etc. that I don't currently need on him and all the crafting stuff on the other guy. Whenever my inventory fills up I sell off the crap, keep the HQ stuff, and possibly sell whatever I have that might be worth something. All the crafting ingredients can be a huge inventory hog unless you have some kind of focus on what you're trying to accomplish. Try not to keep ingredients around that you might use at some point and when gathering try to concentrate on one or only a couple of specific things (like whatever you need for crafting/ whatever sells best) and disregard everything else. Unless you're trying to complete your crafting logs it shouldn't be difficult to keep the clutter to a minimum.