I use a general tool roll, and 2 for wrenches (Metric and SAE) from Bucket Boss. Socket rails for, well, sockets. Those and the drivers go inside an old Craftsman plastic tool box that once housed my Dremel (that stays at home). The 3 rolls and socket box, along with a 2 lbs. hammer, tape, 6" C clamp all fit into a Pelican 1500. Another one behind it stores spare nuts and bolts, spare parts, oil filter, zip ties, etc. The cases are somewhat heavy to lug around, but doable out on the trail. I also have a magnetic hanger for shop towels and a magnetic tray for bolts. They just stick on the steel bits in the cargo area.
There driver's door has a small zippered pouch for tools that are used most often. It includes wire cutters, screwdrivers, and a 3/4" wrench to get the Hi Lift off the bumper. Those used to be in the other tool roll, but they're so much more convenient up front. I also keep a small Craftsman ratcheting T-handle driver with bits for Torx, Philips, and Flat heads screws. It doesn't get used as often, but it (and work gloves) keep everything from shifting around in the door pocket.
There are a million ways to organize your stuff, and everyone has a system that works for them. I'm always keeping an eye out for a new way to implement a storage solution, but have been pretty happy with the current setup.