I've been experimenting with getting sharper images front to back with a pretty easy workflow in Photoshop. There are some really expensive programs out there to do this, but it is not hard to do right in Photoshop cs5 or cs4 (which is what I use.)
These are taken with 45mm lens, f/4.5, 1/90 sec. I took nine photos and began by focusing in front of the first bottle, then deepened my focus until I was focusing on the chair in the background.
I then open the photos in Camera Raw, make some minor adjustments in clarity and whatever else needs it. Select all and synchronize the adjustments and hit DONE. Select them all again in Adobe Bridge >tools>Photoshop>load files into photoshop layers. Wait....
Then, edit>auto-align layers>auto>no check lens corrections.
Then edit>auto blend layers>stack images>check seamless tone and colors.
If done correctly, a sharp image (front to back) will unfold in front of you. I missed a couple focus spots on mine, like the last little jar of Tarahumara corn; kind of fuzzy. (Second jar is Hopi magic corn, first is a variety of Hopi melon.) Yes, I save my seeds. (Watch out Monsanto!)