Just going by feel here are my thoughts. I am weigh 200 pounds. I went with a 185f/185r on my sir9 ss and a185f/160r on my geared Karate Monkey. These rotor sizes are not overkill at all. The rotors don't get overwhelmed by the increased wheel size and seem to handle their braking duties like a 160mm on a 26er. Bottom line . . . I really like having 185s and its more fun to ride when I can brake with gusto or with one finger while the other three and my thumb hold on for dear life!!!
On paper, here's why I think it's reasonable to go up a rotor size when going to a 29er . . .
When braking, the force created between your tire tread and the trail acts on a 11.5% longer moment arm for a 29er versus a 26er. The force between the brake pad and a rotor acts on a 15.6% longer moment arm for a 185er than a 160er. So rather than being at a 11.5.% mechanical disadvantage by staying with the same rotor size, I think its good to go up one rotor size when using a 29er wheel where you actually gain a little bit (4.1%) of moment arm to do the same job.
I think rotational mass does make a difference too, but I don't know how to calculate its effect. I'm sure it eats into the 4.1% gain.
I think folks using canti or V brakes don't have to worry about this because rim brakes almost the same distance away from the hub as the tire/ground contact patch.
Finally, I wonder how our hubs will hold up. Has anyone experienced hub failure due to all that 29er rubber on the ground plus bigger rotors????