I was once complimented by a visitor on having the best organized junkyard they had ever seen. It's been a resource to me for many years, wherever I've lived, for years. A few loose ideas:
* If you live in a naturally forested climate, put the junkyard in the trees. Although you will get a slow mulch of leaves and twigs falling, you will not get nearly such a rank mess of weeds, vines, brambles, etc. completely burying everything which happens all the time with the earlier stages of succession in moist climates.
*Plastics resist rain, and fabrics resist sun. Thus, fabric over plastic makes a great durable cover for perishable items like lumber in long-term storage. The other important point is to keep such items up off the ground. Common pallets will work for a year or two, but they are mostly untreated and will
compost away to nothing in a moist climate.
*I would usually keep the area sorted by categories....a pile of lumber, another of miscellaneous metal, an area of long pipes and stakes standing up, a pile of carpets, a stack of glass and windows, and so on. This makes stuff easy to find and your stash will be a lot more useful.
*Periodically, the junkyard would get a purge. If I hadn't had even a plan for something for a couple of years, knew of nobody else that could use it, or it wasn't an item of regular use or had at least a secondary use (like breaking up old lumber for firewood), then I'd move it on. Frequently by inviting all my friends and acquaintances over to go through the "about to go" pile first.