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In the same way there are dedicated programs that will combine multiple images into a pano, there are programs that can stack multiple images that vary only in the distance at which focus is best. It's often called Z axis stacking. The program combines the parts of the image that are in focus to simulate a much greater DOF, such as you'd get from shooting with a much smaller aperture. (I've stacked the Z axis images in Photoshop CS4. The interface may not be as intuitive, but it works.) There are questions of maximum sharpness when shooting with very small apertures (diffraction) , particularly when shooting with a crop sensor camera. Also, a lens may have a small enough aperture to give a deep enough DOF. Stacking images made with different planes of sharp focus saves the day. You ought to be able to find tutorials with a google search. (I confess I stack so infrequently, when I need to stack I have to find a tutorial to remind me how.)
As for selecting portions of an image to not Z axis combine, I'm guessing it ought to be possible to mask parts of the images to leave an area with better bokeh in the result, but I admit I haven't had an image I needed to try it on. Alternately, I know it's possible stack images for a larger DOF and then mask out the leaves and mask in the leaves again from one of the images with the best bokeh, achieving the same effect.
If stacking images is too intimidating, try using a tripod and shooting withe smaller apertures, up to the smallest available.
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