This seems to be focused predominantly on road bikes, so maybe not very applicable to those of us that ride very wide tyres on frames designed for luggage carrying.
On a bike like my Raven Tour, the frame/fork (and the racks bolted to them) have to be fairly stiff to stop the bike flopping around with a full load. Wheels also have to be sturdy to avoid collapse. The obvious way of getting back a reasonable degree of comfort is to use wide, high-quality, low-pressure tyres.
On this kind of bike, other comfort-enhancers can be sprung seatposts (Dan has one on his Nomad), sprung saddles (I fit these on most of the family bikes with relatively upright positions, but don't yet need them on my drop bar bikes), sprung stems (I've tried one in the past and abandoned it because of the play that developed), thick handlebar padding, there are probably a few other methods.
An alternative approach for a load carrying bike is full suspension. I've tried this as well - I had a Moulton APB space frame with spring and damper type mechanical suspension. This had a very rigid frame made of lots of small triangles. The front and rear racks were attached directly to the main frame, so completely suspended. It didn't take quite as much luggage as my large wheel tourers, but was a more stable load platform than my (contemporary) old mountain bike with the old Karrimor solid-wire racks. For me, the two downsides of the Moulton over a Thorn touring bike were the small wheels, which are good enough for road touring, but don't work as big wheels on rough tracks (I often like to take "short cuts") and the wear in the suspension system (this is only an issue in the long term).