Mineral photography is just a great application of what folks call "macro photography" in the photo world. The typical approach to this is the use of macro lenses and extension tubes or bellows (although macro lenses are not strictly required). Whole books have been written on macro or closeup photography (I particularly like the ones by John Shaw). A whole new game is photography through a microscope. This is a topic you can expect to hear more about, since I have a microscope with a third camera tube, and a digital SLR.

The mineral macro photographer has many things working in his favor. In particular his subjects are not crawling around, or being blown about in the wind. There is plenty of time to arrange and rearrange lighting, and with a digital camera it is possible to just experiment and try again and again.

A big issue when doing extreme closeup photography is limited depth of field. In some cases this is a nice effect (many great photos emphasize some central item of interest by throwing everything else out of focus). A solution for times where extensive depth of field is desired is to stack a sequence of digital images taken with various focus settings. This requires some serious computer software support, and a piece of free software called CombineZ5 is widely used for this. CombineZ5 is the older package and is no longer maintained. CombineZM is the active branch.

Sadly, CombineZ only runs under windows, so a linux user like myself is out in the cold. One tip says that the GIMP is able to stack images using Gimp: Filters->Combine->Depth Merge but I have not looked into this.
Happily, CombineZ is open source under the GPL, so a project could be launched to port this to linux, however this task should not be underestimated. The visual studio CPP environment almost seems to be engineered to make porting difficult. For details, click this Windows Software Porting link.