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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 ...

There is a good article about focus stacking using command line tools align_image_stack and enfuse (both included in Hugin).

Always use as much data as you can. It's actually easier to reduce noise when there's more information to begin with. (Reducing resolution is a brute-force noise removal tool, throwing away both noise and signal.) If you're concerned about the size final image, reduce the resolution at that point.

IMO focus stacking isn't very useful for landscape photography, it's more useful in macro photography, but for landscapes there are better ways to get good focus. check out this online depth of field calculator to get an idea about DOF in different settings. Anyways, about your question, I must say it's possible to get a good result in focus stacking if you ...

You are right about the disadvantages of focus stacking, also, the process of taking pictures for focus stacking (taking multiple pictures at different focus ring positions and getting every bit of the picture sharp in at least one picture) can be a bit technically challenging. That is why traditionally landscape photographers solve this issue by using a ...

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 ...

You could, but it wouldn't work exactly as your illustration suggests except in very simple scenes. If the aim is to produce an image that has as much in focus as possible (the traditional purpose of tilt movements), then focus stacking without regard for an imaginary plane of focus is a simple, effective and highly automatable solution. Despite the fact ...

I don't have too much to add, but I have some limited experience with focus stacking on microscopes that I can share. I've done focus stacking on an SEM, the following image is a stack of only two images. I wish I had a third to fill in the blur in the middle. Image of a flower I took with a scanning electron microscope. The near foreground and the 'sky' ...

In CS5, load your images into layers. Select Edit > Auto Align Layers (at macro distances even on a tripod small changes in focus will alter the perspective of each shot) Select Edit > Auto Blend Layers. This will select the sharpest parts of each layer and create a mask. The masks can be quite complex, but it does a very good job. There is an open ...