First of all, thanks everyone for the comments and support. I really appreciate it.
In my original post I mentioned that shorts sans underwear was one of the options I had tried. The problem is that the chamois did uncomfortable things to my nether regions when I was standing (and pedaling) in the saddle.
Now, I had spent several weeks trying various combinations of undergarments, to no avail. I've taken two 16 mile rides since this thread started, both in the suggested commando mode. There is a definite improvement over wearing underwear in terms of comfort and rubbing. However, the aformentioned manhandling of my manhood is unacceptable.
I have some money coming in this weekend and I'm going to hit my LBS to get a real pair of shorts.
Thanks, everyone, for all the help.