As the OP, I just wanted to follow up to answer as many of the questions raised in this thread that I can.
The wheels are Shimano WH-RS10, front and rear. I've checked and they seem true. I have about 3000 miles on them. They're on their second set of tires (25mm Gatorskin in the rear, and 23mm GP4000 up front). I'm 6'2" and 185. I have checked to verify that the wheels are sitting fully in the drop-outs, and that the skewers are tight. I believe there's enough free play in the brakes. When actuated firmly (but not skid-firm) the brifters are 2/3rds of the way to touching the bars.
Spoke tension is a possibility, I suppose. I'm not proficient in dealing with that. I guess I could take it into my LBS and let them check it. They all "ring" approximately the same tone when plucked.
haha
There seem to be no cracks or anything on the wheels.
With the bike stationary, if I press my thumb against the side of the wheel I can push the wheel until it touches the brakes from either side, without too much effort. But then again, I have no idea what would constitute "too much effort."
Up until a month or so ago, when I noticed rubbing it was always just a matter of the calipers not being centered. But now the calipers are centered, and I feel the rubbing on strong starts, such as when I'm pulling away from a light up a grade with traffic on my tail (motivation to jump on it).
Dave