How can I get the most possible depth of field out of close-up/macro shots?

I own a Nikon D40X and just the kit lens and I'm considering buying either a macro lens or some extension tubes. I don't necessarily want to do true 1:1 macro, just some close ups of bugs, fungi and flowers.

Answer

Use focus stacking for static scenes; a small aperture and matching combination of ISO/lighting for scenes with moving elements. Focus stacking is more time consuming, but preferred because small apertures will introduce diffraction.

When photographing flowers outside, you might want to build a temporary wall to block wind so your flower would be static.

Using shorter focal length also helps, but due to closer distance it makes lighting more difficult and may scare your model.