Another option, which I have used before (though more as a reaction to chaffing rather than prevention-would work either way) is to tape up the spot. I use a soft white mesh tape (can't remember what its called, but its also what the Australian Army dishes out to soldiers in copious quanitities to put over blister dressings to hold them down), which I cut into lengths of about 8 inches. It sticks pretty well, to body hair aswell-which can make it painful to remove-I do it in the shower, or you could wait for it to come off naturally, as you wouldn't get many showers on a long through hike. if you round the edges off, then the chances of it coming loose are reduced. Also, if you shave (or wax) the site first, you will reduce the chance of it sticking to any hair for a fair while.
FYI I normally get my chaffing on my thighs, pretty high, but not quite at the nether regions; not high enough for boxer briefs to cover it all effectively, unfortunately.
If your normal chaffing (not the spandex-induced but crack stuff) is more on your nether regions, things are probably a bit more complicated. Waxing for starters is alot more painful, and tape would be more difficult to apply, and remove.
I hate chaffing.
Another option again is to get skinnier and lose weight. I only started chaffing a couple of years ago after I started going to the gym and training with extreme pack weights-my body adapted of course and I think I've almost doubled the size of my legs since then. So they rub. Stick thin marathon runners might have less of a problem.