Body parts are mostly identical to 1/2 tons, other than the already mentioned spears. In the last six months I've seen good spears for 3600's listed on ebay 3 or 4 times, so difficult but not at all impossible. If it's a longbed like mine, those parts are available, but pricey.
The real problems are the suspension and drive train. The springs seem to be tough to find. Most vendors only list 1/2 ton. The wheels were tough as well. I upgraded mine, and had only a limited number of choices due to the backspacing. Most of the bearings are available at Napa, but good luck rebuilding your rear end using new parts from the vendors if you need to.
The resale value depends where you live, I think. I've had numerous people interested in mine once they realize it's the 3/4 ton.
Overall, I love the heavier-duty truck. The hard ride is fine, it's a truck! I threw on some softer tires and it's 150% better than stock. The lower gears are only issue in that I can't freeway it, but my daily commute is 2.5 miles, so that has only been an issue a few times. The fact that I can throw a huge load of pavers at it, for example, and it doesn't blink an eye, is great.