I keep a black plastic crate in my trunk, in which are some towels, rope, 12V air compressor, etc. I used to secure the crate with an array of bungee cords, but that's obviously not a great solution.
This last weekend I decided to bold the sucker down so I could ditch the bungee cords. I went to Home Depot and bought a 5/16" hex head bolt (1.5"), a matching nut, and 2 washers. Total cost was about $0.50.
I did some measuring and hole-cutting with an X-acto knife... a small hole in the trunk carpet, and a small hole in the bottom of the crate let me use the pre-cut holes in the fiberboard floor material to anchor things. Does that make sense? Lift up the carpet and you'll see fiberboard over the spare. Use one of the small slots in it... one is perfectly placed for this. Run a bolt up through the slot in the board, the carpet, and the crate. Make sure you use washers on each side.
(BTW the hole in the carpet -- more of a slit -- is barely visible. I'll do worse to that carpet accidentally, I'm sure.)
So anyway I have a functional, cheap, and only moderately ugly storage unit in the trunk that won't bounce around. There is a bolt & nut poking through into the crate, but since I always keep a towel in there I just put the towel on the bottom.
I may mount another one on the other side of the trunk. Supplements the cargo net well. If I need to remove them, it just takes a moment with a a couple of tools (one to hold the bolt head under the floorboard, one to twist the nut topside). Eventually I may secure the bolt head so I don't need a tool to hold it down, and put a wing nut on tne top side for a tool free removal.
I thought about using industrial velcro, but I didn't want the carpet to be a load-bearing component. Good adhesion would also be a problem.
This is the only mod I have done to my car.