I have most of my boxes, flattened most of them, only missing a couple from when I first came out of my dark age and any BL buys without boxes.
I was keeping bags and cardboard boxes but I had already thrown so many out I found it useless to start now.
My shipping boxes either are storing LEGO or other misc. items, I also have the ads included in S@H boxes.
I too have all the LEGO Store bags. You did forget to mentioned used sticker sheets. I have all those too. Also have all the poly bags from promo sets, etc., LEGO Store Calendars, etc. Pretty much anything that says LEGO on it.