A lot of good suggestions here, but I can't believe I got to the end of the thread so far and nobody mentioned my particular nit pick: a lockable glove box.
Being down south, I drive with the top off most of the time. Every time I stop somewhere Iv'e got to lug wallet, cell phone, sunglasses, radar detector and any other little stuff I can't leave out in plain sight in an open car.
Yes, I can always gather it all up and toss it in the trunk, but that's a real PITA, especially when I forget something is back there and start slinging it all over the place while driving.
I know Shinoo is working on one, so I'll take it any way I can get it.