What are the best practices for DOF stacking? How do you get the frames with focus just right amount apart? How do you stack them in post processing?
If you are taking photos of something stationary, then a focusing rail will allow you to do them perfectly. If you are talking about moving things, like insects, then all you can do is take a lot of photos. If you aren't able to focus reliably without a tripod and rail, then you can use burst mode. But, with some practice, you can get to the point where you can reliably click the shutter when specific portions of the shot are in focus and capture a series that way instead.
3What about post processing?– KarelJul 22, 2010 at 2:47
I agree with that remote is a must. Jul 23, 2010 at 17:23
There is a good article over at DPS about focus stacking which documents one way of doing it including post processing in Photoshop.
There is a good article about focus stacking using command line tools align_image_stack and enfuse (both included in Hugin).
A friend of mine recommended ImageJ in combination with the Stack Focuser plugin for combining the images into a single image with an extended depth of field. He mainly uses it for microscope images.
I've also found good references for CombineZP. Although there's not much info on the site there is a yahoo user group for it for more information and this (old) article describes a complete workflow using CombineZP.
I think it is worth mentioning that if you are a Canon person, Magic Lantern has a great focus stacking utility that will let you set the number of shots in front and the number behind as well as the size of the focus shift for each shot. It will take the series of shots and even generate a little script that can be used with Hugin to merge.