I take advantage of nooks in my trunk to stash my gear and were possible I hold it down with bungee cords. The trunk in one of my cars (Crown Victoria) happens to be missing the lining, so that opens up access to some significant cavities in the fenders.

There are a veriety of commercial solutions available at auto parts stores and stores like "Hold Your Own" that can organize your trunk or cargo area pretty effectively. You just have to figure out what will work best with your particular vehicle. There are braces that stick to carpeting and bins, bags, etc.

One thing I have used in a variety of vehicles with great success is a standard plastic milk crate. For some reason they don't slide around or tip over very easily. Of course they will slide on steel, but if you have carpeting or a rubber mat, they stay put.