|Interesting question.... I'll preface my remarks by noting that, from what I've seen on eBay, a true treasure can sell for a pittance, while useless clutter might sell for a medium-sized fortune.
Generally, I'd expect that high-value used parts would be those that normally degrade due to time, and for which there are no real replacements: dashboards, crash rolls, seat foam, some switches, some critical transmission and rear end parts.
Less expensive parts would be more or less unique to the JH and currently in low supply: working transmissions, brake calipers and rear drums, a few suspension parts, body parts such as fenders, doors, hoods, stainless steel bumper tops, some trim items, major rust repair panels.
Items which may be found in quantity in the wrecking yards and for which spares may still be available should be of rather low value: distributors, engines, bellhousings, clutch parts, carburetors, pedal carriers, steering wheels, heater boxes, lights and lenses, door handles, most suspension parts, most interior and exterior trim, factory wheels, and the like.
Of course some items are inherently more expensive than their availability would indicate: for example, original virgin windshields and door glass, good running engines, 5-speed transmissions, and so on.
Used expendables/consumables are unlikely to be worth the trouble of selling. Some items are (nearly) worthless individually, but might be profitable if bundled together with a low starting bid. As an example, "everything for the left door -- handles, knob, slider, arm rest, screws and bolts, trim, push fixes, washers, etc. -- starting bid only $13.00. A few small items might be missing. Does NOT include the door itself, hinges, upholstery, glass, glass channels, or regulator." This would be $20-$25 in parts, for which you might, if lucky, get $30-40. But you'd make a sale and have a happy customer who'd be a lot more inclined to bid on an expensive item later.
I agree that a lot of JH parts are being offered at too high a starting price, particularly by some of the wrecking yards -- for example, one well-known place almost invariably asks at least twice what I've repeatedly seen the item sell for elsewhere. Perhaps their business model relies primarily on desperation sales, or maybe they consider eBay as little more than inexpensive advertising for a physical storefront. Certainly it would seem difficult to sell things at auction if people won't bid.
In summary, if you want to make even a modest profit on parting out a single car, you'll have to give very careful thought to your pricing scheme. My personal recommendation would be to set your opening bids at 1/2 to 2/3 the low side of fair market value. And at least for the smaller items, list your best guess as to shipping charges up front. I strongly suggest you avoid nebulous 'handling fees' -- I'm usually quite understanding about the high cost of packaging and shipping things nowadays, but quite refuse to consider paying someone $25-$50 an hour in addition to that, so that they can toss something into a Post Office mailer.
Finally, for the various categories above, the examples given were picked essentially at random, with no attempt to determine relative scarcity.