I keep a lot of stuff in my trunk. To keep all my tools from rolling around and generally monopolizing the trunk space, I built a false floor for the trunk with cubbies.
I wanted this organizer to fit as perfectly as possible, so I spent about an hour recreating my trunk in CAD. Using this model, I designed a box that balanced being a snug, perfectly contoured fit with being actually possible to make. Using 1x6in pine, I built the frame/walls for the 1/2in plywood lids to sit on.
I ended up with a bunch of extra plywood, so I made some bins for stuff like metalworking tools, ratchet straps and other miscellaneous items.