I read a patent a couple of years ago about reducing drag with a half tonneau cover (just the back half.) it's supposed to work better than a full cover. The counter-intuitive part is you leave the front of the the box created by the cover and bed and tailgate *open* (and the tailgate closed.) I have a scrap of plywood in the garage that looks about the right size but I haven't tried it yet -- would have been handy a couple of weeks ago when I took a long trip. As an added bonus, it'll keep the rain off my luggage thrown in the back.
Not surprising. The tailgate up reduces drag (for modern trucks) by creating a vortex area of higher pressure, but low flow that enables the air going over and around the cab to flow smoothly back (around the vortex) and not impact the tailgate. A back-half tonneau cover would do something similar, by both creating the high pressure zone in the front of the bed (possibly at lower flow than having the whole bed open), while minimizing area for any bleed flow to hit.
The best would obviously be a cap that slopes downward at approx a 15deg angle, then has a K-tail at the rear to create a vortex trail to reduce wake drag.
A K-tail is the slope plus moderate flip-up seen at the back of hatchbacks designed for mileage, like a Prius. What it does is truncate an ideal teardrop-end but create a high pressure vortex that virtually recreates it and reduces wake drag.
http://en.wikipedia.org/wiki/KammbackAlso the logic of boat-tail bullets :)