When you can't use a tripod what do you usually do? I most of the time analyze the scene of a single exposure can capture the entire dynamic range without sacrificing my low ISO settings. If is is not possible, I crank up the ISO to a level where the highest exposure's shutter speed is well above 1/40. This is to avoid any camera shake during the shot. Photomatix Pro does a good job aligning the images.
Below is the shot of the Zen Garden of Tenryuji Temple. I was a horrible cloudy day to for us. So, when I saw the clouds clearing up a little, I went back to this area to shoot again. Autumn colors are always amazing.