Last fall, for the first time in my backpacking career, I faced a very unfun experience while backpacking - chaffing. As I explained to my hiking partners who found the situation entirely more comical than I did, I felt like I had been bit in the crotch by a Rottweiler.
At the time, I was wearing Merino Wool underwear by Minus 33 which in the past helped control odor and stood up better to long-term use. I can't say I know what caused the difference as my cleaning habits and temperature control remained the same, but nonetheless I elected to search for a better solution as wearing wool on an area of my body that is fairly vital didn't seem to make a ton of sense. Chaffing is caused by abrasion and made worse through hot and moist environments. So good hygiene and ventilating gear choices both play a significant role to offer the best chance of success.
After a lot of research, I decided to use a combination of synthetic shorts, and synthetic briefs, coupled with periods where I wore only the shorts by themselves while on the move.
For the shorts, I elected to go with the Mountain Hardware Refueler $44 (http://www.backcounty.com/outdoorgear/mountain-hardwear-refueler-short-mens/MHW1165M.html). They are extremely light, pack small, dry quick, are long enough to not look terribly dorky, have a very nice feel to them, and get the job done. They also come with an interior support system (net liner) which helps on those days when I elect to avoid wearing anything else to get the best ventilation possible. I had tried other options and several different offerings from Patagonia almost made the cut, but I dubbed the Refueler as the best for my needs. It comes with only one little "key" pocket in the back, which is helpful, but I do wish it had other pockets. I'm not quite sure why as I have a pack on my back full of stuff, but I guess I just like compartmentalizing things. And no, please don't recommend a pair of Umbro's or running shorts as they offend the trees just as much as they offend the general public.
Researching underwear was a lot tougher because it was a next-to-skin layer that needed to be more performance-based. I've known about nano technologies and silver treatments for awhile which are being used in Europe and tested with the U.S. military. These high-tech attributes help with stink control and longevity. Unfortunately, they are hard to find and are very costly. In the end, I decided to go with the ExOfficio Boxer Briefs $25 (http://www.rei.com/product/694431). This shouldn't be confused with many other similar named products from ExOfficio and is worth noting that I think ExOfficio may very well be discontinuing this product. I found the tighter these briefs the better. There are other simlar products from Under Armour and others, but I found the ExOfficio to offer the best all round performance.
If necessary, other anti-chaffing tools include treatments with Hydropel (http://www.backpackinglight.com/cgi-bin/backpackinglight/hydropel.html), BodyGlide (http://www.amazon.com/bodyglide-anti-chafing-stick/dp/B001FSL8MA), or my new favorite because it comes in such a small and useful package, BandAid Friction Block Stick (http://www.bandaid.com/productList.do?typeID=4).