I always make it a point to put the maximum possible strain on the tendons running through my wrists, no matter what I do. Using an input method that is not sufficiently taxing for my moving parts surely cannot be anything but a wasted opportunity. The Sixaxis is just too light!
No, actually, I grab the first thing that I find within reach when I'm just goofing around the store and such, but I do prefer the Dualshock 3 when I sit down and play a game. As an added twist, I don't care as much when I'm playing PixelJunk Monsters. Uncharted though ... rawr.